Well, first of all, can someone tell what server is causing this issue? Yahoo? Currently I'm using few email accounts (1 POP, at least 2 IMAP and 2 MfE) and I never had this issue (I'm using it longer then you guys, so believe me ), but I do not use Yahoo.
It looks like a problem in the backend (UI only shows something, that stored in the QMF DB).

So, can someone describe the problem step by step? In addition it would be nice to get a messageserver logs and QMF DB, but I think I'm asking too much :-D