I had the exact same problem like the original poster. It all started two weeks ago as well. Funny coincidence. I did not know what to do then and I reflashed including mmc after I figured out how to backup my angry birds scores. Yes they are important :-).

Reflashing helped of course and both of my imap accounts are downloading again. One thing still bugs me though. When I manually sync mails the little white arrow next to the clock is not appearing anymore. I had the same problem two weeks ago when sync stopped working completely. Its still syncing now though.

rm -rf /home/user/.qmf does not work even with root access. Lots of permission denied errors. I hoped it would help me getting my white arrow back. Whoami shows root after devel-su.

Edit:
I tried to run "rm -rf .qmf" as the normal user and it worked. I reebooted and my mail folders where empty. I tapped the sync button and the white sync arrow was showing and all the latest mails were downloading. And consecutive syncs are much faster, because the mail database is slim again I guess. Perfect.

I hope this works for the original poster as well. I will now once a month clear my .qmf folder to keep the mail app in shape.