Still affects 12.04 release. This is manual FIX.

I stuck on that problem when building my mini-itx atom backend platform with 
RAID and LVM. Inspired by workaround of bug 976509 given in comment #8 I 
started filenames investigation. File name of missing package 
"fs-secondary-modules-..." was TRUNCATED TO 65 CHARS. In my case file on 
flashdrive looked like this:
"pool/main/l/linux/fs-secondary-modules-3.2.0-23-generic-pae-di_3.2.0-23.36_i386.ude"
but extension should be "udeb" instead of "ude"!
Note that you can find more 65-chars names truncated that wrongly ends with 
"ude",  so search & fix them all.

12.04 alternate may fail later on installing package "xserver-xorg-video-ati" 
(bug #789898 resurrection?).
 In my case it was due to another wrongly mangled filename. I found package 
name misspelled, it was 
"xserver-xorg-video-radeon_6.14.99~git20111219.aacbd629-0ubunt_i386.deb"
but should be
"xserver-xorg-video-radeon_6.14.99~git20111219.aacbd629-0ubuntu2_i386.deb"
note truncation before suffix "_i386.deb"

After that one I could successfully finalize installation.

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https://bugs.launchpad.net/bugs/927285

Title:
  Precise Alternate USB install fails, expecting to find CD-ROM

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