@costinel: have you made sure you manually set that option to 'true'? It's 'false' by default. For the record, this is what it looks like with a completely fresh vagrant VM for Ubuntu Precise.

vagrant@vagrant-ubuntu-precise-64:~$ sudo unattended-upgrade --debug
Initial blacklisted packages:
Starting unattended upgrades script
Allowed origins are: ['o=Ubuntu,a=precise-security']
adjusting candidate version: '<Version: package:'ntpdate' version:'1:4.2.6.p3+dfsg-1ubuntu3.6'>'
Checking: ca-certificates (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: cpio (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libc-bin (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libc-dev-bin (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libc6 (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libc6-dev (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libgcrypt11 (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libgnutls26 (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: libssl1.0.0 (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: linux-headers-generic (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: linux-headers-virtual (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: linux-image-virtual (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: linux-libc-dev (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: linux-virtual (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: multiarch-support (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: openssl (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: perl (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: perl-base (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
Checking: perl-modules (["<Origin component:'main' archive:'precise-updates' origin:'Ubuntu' label:'Ubuntu' site:'archive.ubuntu.com' isTrusted:True>", "<Origin component:'main' archive:'precise-security' origin:'Ubuntu' label:'Ubuntu' site:'security.ubuntu.com' isTrusted:True>"])
pkgs that look like they should be upgraded: ca-certificates
cpio
libc-bin
libc-dev-bin
libc6
libc6-dev
libgcrypt11
libgnutls26
libssl1.0.0
linux-headers-generic
linux-headers-virtual
linux-image-virtual
linux-libc-dev
linux-virtual
multiarch-support
openssl
perl
perl-base
perl-modules
Fetched 0 B in 0s (0 B/s)
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 4412350 DestFile:'/var/cache/apt/archives/perl_5.14.2-6ubuntu2.5_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/p/perl/perl_5.14.2-6ubuntu2.5_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/perl_5.14.2-6ubuntu2.5_amd64.deb')
found pkg: perl
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 1512922 DestFile:'/var/cache/apt/archives/perl-base_5.14.2-6ubuntu2.5_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/p/perl/perl-base_5.14.2-6ubuntu2.5_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/perl-base_5.14.2-6ubuntu2.5_amd64.deb')
found pkg: perl-base
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 3397434 DestFile:'/var/cache/apt/archives/perl-modules_5.14.2-6ubuntu2.5_all.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/p/perl/perl-modules_5.14.2-6ubuntu2.5_all.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/perl-modules_5.14.2-6ubuntu2.5_all.deb')
found pkg: perl-modules
conffile line: /etc/perl/Net/libnet.cfg fb2946cae573b8ed3d654a180d458733
current md5: fb2946cae573b8ed3d654a180d458733
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 84736 DestFile:'/var/cache/apt/archives/libc-dev-bin_2.15-0ubuntu10.13_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/e/eglibc/libc-dev-bin_2.15-0ubuntu10.13_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libc-dev-bin_2.15-0ubuntu10.13_amd64.deb')
found pkg: libc-dev-bin
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 2942780 DestFile:'/var/cache/apt/archives/libc6-dev_2.15-0ubuntu10.13_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/e/eglibc/libc6-dev_2.15-0ubuntu10.13_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libc6-dev_2.15-0ubuntu10.13_amd64.deb')
found pkg: libc6-dev
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 1179462 DestFile:'/var/cache/apt/archives/libc-bin_2.15-0ubuntu10.13_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/e/eglibc/libc-bin_2.15-0ubuntu10.13_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libc-bin_2.15-0ubuntu10.13_amd64.deb')
found pkg: libc-bin
conffile line: /etc/gai.conf 629c0e2f8276b26c29b95f7ed53074d7
current md5: 629c0e2f8276b26c29b95f7ed53074d7
conffile line:  /etc/default/nss d6d5d6f621fb3ead2548076ce81e309c
current md5: d6d5d6f621fb3ead2548076ce81e309c
conffile line:  /etc/ld.so.conf.d/libc.conf d4d833fd095fb7b90e1bb4a547f16de6
current md5: d4d833fd095fb7b90e1bb4a547f16de6
conffile line:  /etc/bindresvport.blacklist d2d1b996add35b65f64a22e9c8413632
current md5: d2d1b996add35b65f64a22e9c8413632
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 4637060 DestFile:'/var/cache/apt/archives/libc6_2.15-0ubuntu10.13_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/e/eglibc/libc6_2.15-0ubuntu10.13_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libc6_2.15-0ubuntu10.13_amd64.deb')
found pkg: libc6
conffile line: /etc/ld.so.conf.d/x86_64-linux-gnu.conf 593ad12389ab2b6f952e7ede67b8fbbf
current md5: 593ad12389ab2b6f952e7ede67b8fbbf
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 857448 DestFile:'/var/cache/apt/archives/linux-libc-dev_3.2.0-99.139_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-libc-dev_3.2.0-99.139_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-libc-dev_3.2.0-99.139_amd64.deb')
found pkg: linux-libc-dev
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 1055214 DestFile:'/var/cache/apt/archives/libssl1.0.0_1.0.1-4ubuntu5.35_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/libssl1.0.0_1.0.1-4ubuntu5.35_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libssl1.0.0_1.0.1-4ubuntu5.35_amd64.deb')
found pkg: libssl1.0.0
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 282352 DestFile:'/var/cache/apt/archives/libgcrypt11_1.5.0-3ubuntu0.5_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/libg/libgcrypt11/libgcrypt11_1.5.0-3ubuntu0.5_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libgcrypt11_1.5.0-3ubuntu0.5_amd64.deb')
found pkg: libgcrypt11
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 460004 DestFile:'/var/cache/apt/archives/libgnutls26_2.12.14-5ubuntu3.12_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/g/gnutls26/libgnutls26_2.12.14-5ubuntu3.12_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/libgnutls26_2.12.14-5ubuntu3.12_amd64.deb')
found pkg: libgnutls26
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 12888562 DestFile:'/var/cache/apt/archives/linux-image-3.2.0-99-virtual_3.2.0-99.139_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-image-3.2.0-99-virtual_3.2.0-99.139_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-image-3.2.0-99-virtual_3.2.0-99.139_amd64.deb')
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 4482 DestFile:'/var/cache/apt/archives/multiarch-support_2.15-0ubuntu10.13_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/e/eglibc/multiarch-support_2.15-0ubuntu10.13_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/multiarch-support_2.15-0ubuntu10.13_amd64.deb')
found pkg: multiarch-support
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 116164 DestFile:'/var/cache/apt/archives/cpio_2.11-7ubuntu3.2_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/c/cpio/cpio_2.11-7ubuntu3.2_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/cpio_2.11-7ubuntu3.2_amd64.deb')
found pkg: cpio
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 524104 DestFile:'/var/cache/apt/archives/openssl_1.0.1-4ubuntu5.35_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/o/openssl/openssl_1.0.1-4ubuntu5.35_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/openssl_1.0.1-4ubuntu5.35_amd64.deb')
found pkg: openssl
conffile line: /etc/ssl/openssl.cnf ce31ab5015842bf7c2939514a634e0e4
current md5: ce31ab5015842bf7c2939514a634e0e4
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 208000 DestFile:'/var/cache/apt/archives/ca-certificates_20160104ubuntu0.12.04.1_all.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/c/ca-certificates/ca-certificates_20160104ubuntu0.12.04.1_all.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/ca-certificates_20160104ubuntu0.12.04.1_all.deb')
found pkg: ca-certificates
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 11708302 DestFile:'/var/cache/apt/archives/linux-headers-3.2.0-99_3.2.0-99.139_all.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-headers-3.2.0-99_3.2.0-99.139_all.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-headers-3.2.0-99_3.2.0-99.139_all.deb')
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 978332 DestFile:'/var/cache/apt/archives/linux-headers-3.2.0-99-generic_3.2.0-99.139_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-headers-3.2.0-99-generic_3.2.0-99.139_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-headers-3.2.0-99-generic_3.2.0-99.139_amd64.deb')
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 977126 DestFile:'/var/cache/apt/archives/linux-headers-3.2.0-99-virtual_3.2.0-99.139_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux/linux-headers-3.2.0-99-virtual_3.2.0-99.139_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-headers-3.2.0-99-virtual_3.2.0-99.139_amd64.deb')
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 2608 DestFile:'/var/cache/apt/archives/linux-headers-generic_3.2.0.99.115_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux-meta/linux-headers-generic_3.2.0.99.115_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-headers-generic_3.2.0.99.115_amd64.deb')
found pkg: linux-headers-generic
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 1762 DestFile:'/var/cache/apt/archives/linux-virtual_3.2.0.99.115_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux-meta/linux-virtual_3.2.0.99.115_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-virtual_3.2.0.99.115_amd64.deb')
found pkg: linux-virtual
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 2692 DestFile:'/var/cache/apt/archives/linux-image-virtual_3.2.0.99.115_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux-meta/linux-image-virtual_3.2.0.99.115_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-image-virtual_3.2.0.99.115_amd64.deb')
found pkg: linux-image-virtual
<apt_pkg.AcquireItem object:Status: 2 Complete: 1 Local: 1 IsTrusted: 1 FileSize: 2620 DestFile:'/var/cache/apt/archives/linux-headers-virtual_3.2.0.99.115_amd64.deb' DescURI: 'http://archive.ubuntu.com/ubuntu/pool/main/l/linux-meta/linux-headers-virtual_3.2.0.99.115_amd64.deb' ID:0 ErrorText: ''>
check_conffile_prompt('/var/cache/apt/archives/linux-headers-virtual_3.2.0.99.115_amd64.deb')
found pkg: linux-headers-virtual
blacklist: []
InstCount=23 DelCount=0 BrokenCout=0
Packages that are upgraded: ca-certificates cpio libc-bin libc-dev-bin libc6 libc6-dev libgcrypt11 libgnutls26 libssl1.0.0 linux-headers-generic linux-headers-virtual linux-image-virtual linux-libc-dev linux-virtual multiarch-support openssl perl perl-base perl-modules
Writing dpkg log to '/var/log/unattended-upgrades/unattended-upgrades-dpkg_2016-03-03_14:13:56.579920.log'
adjusting candidate version: '<Version: package:'ntpdate' version:'1:4.2.6.p3+dfsg-1ubuntu3.6'>'
marking linux-headers-3.2.0-98-generic for remove
Packages that are auto removed: 'linux-headers-3.2.0-98-generic'
(Reading database ... 97350 files and directories currently installed.)
Removing linux-headers-3.2.0-98-generic ...
dpkg: warning: while removing linux-headers-3.2.0-98-generic, directory '/lib/modules/3.2.0-98-generic' not empty so not removed.
Packages auto-removed
InstCount=0 DelCount=1 BrokenCount=0