I pulled in ubuntu-9.10-rc-server-i386.iso, and built a virtual machine using that. I set up the openssh server only. I did not use an apt-cache installation. Using the supplied sources.list, I installed apt-file.

root@apt-file:~# apt-file --version
apt-file version 2.2.2
(c) 2002 Sebastien J. Gross <email address hidden>

root@apt-file:~# 

root@apt-file:/var/log# ll /var/cache/apt/archives/apt-file_2.2.2_all.deb
-rw-r--r-- 1 root root 26610 2009-04-28 17:05 /var/cache/apt/archives/apt-file_2.2.2_all.deb
root@apt-file:/var/log# 


Testing per my original entry, I still don't see the Contents file on the CD-ROM:

root@apt-file:~# find /cdrom/* -iname Contents-i386.gz
root@apt-file:~# 

Updating apt-file produced:

root@apt-file:~# apt-file update
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.gz
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.gz
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.gz
File is up-to-date.
Downloading complete file http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.gz
Downloading Index http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.gz
File is up-to-date.
Downloading Index http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.gz
File is up-to-date.
root@apt-file:~# 


I then mounted the CD-ROM and enabled it by uncommenting it in sources.list. I then updated again.

root@apt-file:~# apt-file update
Put CDROM labeled [Ubuntu-Server_9.10__Karmic_Koala__-_Release_Candidate_i386_(20091020.3)] in the cdrom device
read: 1: arg count
mount: block device /dev/sr0 is write-protected, mounting read-only
mount: /dev/sr0 already mounted or /media/cdrom0 busy
mount: according to mtab, /dev/sr0 is already mounted on /media/cdrom0
cp: cannot stat `/cdrom/dists/karmic/Contents-i386.gz': No such file or directory
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic/Contents-i386.gz
File is up-to-date.
Downloading Index http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://us.archive.ubuntu.com/ubuntu/dists/karmic-updates/Contents-i386.gz
File is up-to-date.
Downloading Index http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.gz
File is up-to-date.
Downloading Index http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.gz
File is up-to-date.
Downloading Index http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.diff/Index:
No Index available.
Downloading complete file http://security.ubuntu.com/ubuntu/dists/karmic-security/Contents-i386.gz
File is up-to-date.
root@apt-file:~# 

Note that apt-file still works for packages on the CD-ROM. I expect that this is because it uses package data from the repository, not from the CD-ROM. If so, this could cause a problem for systems which are not upgraded after installation.