Hi,
I'm possibly having the same problem - please refer to this thread for more information regarding this:-
http://discussions.apple.com/thread.jspa?threadID=588951&tstart=0
("Phantom Blank Spam blocking Mail from retrieving new mail in Apple Mail")
The problem seems to revolve around blank email messages being received into a server-side inbox. These blank messages, presumably some form of spam have no sender, no recipient, no date, no source code, no body text and no subject.
These 'phantom' blank emails appear to be the root of the problem as once they are manually removed the our server-side inbox (either through Apple Mail's 'Get Info' / 'Remove from Server' (Server settings) function, or via the ISPs webmail facility), the email starts picking up mail automatically again–immediately, without any other intervention other than clicking 'Get Mail'. Until they are removed, Apple Mail will NOT collect any more mail, automatically or manually through 'Get Mail'.
Please check to see if you have any such messages. I'd be interested to know if this is a scenario dependent on 'phantom email' or ISP specific.
Best wishes
Jamie