I've been having problems with qpopper corrupting mailboxes when a user is at their disk quota. Here's the background;
Yes, this happens to us on a weekly basis, too. I find that the mailbox can be pretty much reconstructed using a combination of the temp pop drop and part of the corrupted spool file. If you want, i can supply the exact steps i use to do this. There's a chance that a message or two might get lost in this process, but i don't sweat it too much anymore. Though it would be nice if the problem never came up in the first place.
-Matt
