Mail deleting messages, settings changing

Messages in Mail (MacBook OS X 10.7.3) are being deleted from both the inbox and sent mail on both Mail and the server (Yahoo! - using IMAP).

I have configured mailbox behavior settings to save all messages, drafts and sent mail on both the server and the Mail client; these are not messages that I have deleted (nor do they appear in "trash").

Additionally, settings in "mailbox behavior" are sometimes changing on their own (like "save drafts to server" becomes unchecked).

And finally (unrelated), message formatting is sometimes changed in Mail (although maintained if I read the message on the server)

Attempted solutions: A couple of weeks ago I went to the Genius Bar. With advice from the Genius guy, I backed up the computer with Time Machine and then reinstalled the OS. The problem persisted so, with Genius help, I deleted mailbox preferences in the library and deleted all accounts in Mail. The problem has continued. I have emailed Yahoo! - but they have not been able to offer a solution either.