What version of Mail::IMAPClient are you running? MARKOV recently took over maintainership of the module, which is good because he's written some very useful mail modules already. If you haven't upgraded to the lastest version 3.02, give that a spin and see if that works for you.

If you're already running MARKOV's version, try backreving to the last version by DJKERNEN 2.2.9. MARKOV has been doing some rewriting, so it might help flush out any potential bugs in his new code.

I would test it near the end of your script by grabbing a list from $imap->seen and comparing it to @msgs in your code to make sure the "Seen" flag was really changed.