I also was affected and it was fairly annoying. I managed to workaround
following this thread http://ubuntuforums.org/showthread.php?t=12737,
altough you end up with apt complaining with "serious warnings". I found
out that you can pass the serious warnings if you reinstall each package
affected by the serious warning. I'm not at home now, so I can't paste
the warnings I'm talking about and the script I plan to use, but I plan
to do i shortly (week end).

-- 
files list file for package `*' is missing final newline
https://bugs.launchpad.net/bugs/108189
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