Update manager does not show all updates

[Orzech]

1) Ubuntu version:
Description: Ubuntu 16.04 LTS
Release: 16.04

2) Package version:
update-manager:
  Installed: 1:16.04.3
  Candidate: 1:16.04.3

3) Expected scenario:
Update manager should show all available updates.
4) What really happens:
Update manager does not show the following updates (listed with "sudo apt list --upgradeable"):
bind9-host/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
dnsutils/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libbind9-140/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libdns-export162/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libdns162/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libisc-export160/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libisc160/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libisccc140/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
libisccfg140/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
liblwres141/xenial-updates 1:9.10.3.dfsg.P4-8ubuntu1 amd64 [upgradable from: 1:9.10.3.dfsg.P4-8]
Instead, I get only some notification that important system updates are awaiting (or something like that), but when I open update manager it tells me that my system is up to date. Before that, I had disabled automatic security updates installation, xenial-backports and multiverse in update-manager.

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[Orzech (piotr.orzechowski)]

Happened again, this time with:
gnome-software/xenial-updates 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1 amd64 [upgradable from: 3.20.1+git20160420.1.ca63436.ubuntu-xenial-0ubuntu2]
gnome-software-common/xenial-updates,xenial-updates 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1 all [upgradable from: 3.20.1+git20160420.1.ca63436.ubuntu-xenial-0ubuntu2]
ubuntu-software/xenial-updates 3.20.1+git20160426.1.a976144-ubuntu-xenial-0ubuntu1 amd64 [upgradable from: 3.20.1+git20160420.1.ca63436.ubuntu-xenial-0ubuntu2]
xinit/xenial-updates 1.3.4-3ubuntu0.1 amd64 [upgradable from: 1.3.4-3]

[Sebastien Bacher (seb128)]

Thank you for your bug report, could you make a screenshot showing the issue?

[Seth Arnold (seth-arnold)]

This sounds a lot like the phased updates: https://lwn.net/Articles/563966/

[Orzech (piotr.orzechowski)]

I've installed Ubuntu in virtual machine and couldn't reproduce the issue with above packages. There was new one invisible fo Update Manager, though. Looks like "phased updates" indeed. I was just expecting GUI and CLI to behave consistently regarding each other.

[Sebastien Bacher (seb128)]

Could indeed be what Seth said, is it still missing for you?

[Orzech (piotr.orzechowski)]

Yes, it happens very often. Now the "invisible" update set is:

brltty/xenial-updates 5.3.1-2ubuntu2.1 amd64 [upgradable from: 5.3.1-2ubuntu2]
libbrlapi0.6/xenial-updates 5.3.1-2ubuntu2.1 amd64 [upgradable from: 5.3.1-2ubuntu2]
python3-brlapi/xenial-updates 5.3.1-2ubuntu2.1 amd64 [upgradable from: 5.3.1-2ubuntu2]
ubuntu-drivers-common/xenial-updates 1:0.4.17.1 amd64 [upgradable from: 1:0.4.17]
xbrlapi/xenial-updates 5.3.1-2ubuntu2.1 amd64 [upgradable from: 5.3.1-2ubuntu2]

I see the "Important system updates awaiting" notification, but when I run Update Manager it says my system is up to date.

[Sebastien Bacher (seb128)]

ok, that's the feature explained before then an not a bug (the notification is an issue though, but not with update-manager since it's not responsible for it, gnome-software takes the blame for that one)