Mail.app mailbox corruption
You could try deleting the "Envelope Index" files.

Run the following Terminal commands to backup and delete the files:

cd ~/Library/Mail/V2/
cp MailData MailData.old
cd MailData
rm Envelope\ Index Envelope\ Index-shm Envelope\ Index-wal


Alternatively…


Quit Mail
In Finder, press ⌘ cmd+⇧ shift+G

Copy and paste the following  

~/Library/Mail/V2/MailData/


Press return or click Go
Backup then delete/move these files to the Trash:


Envelope Index  
Envelope Index-shm  
Envelope Index-wal

Relaunch Mail and wait for messages to import.


Note: once in a while this causes a corrupted message or two to reveal itself, usually in the form of having no "From" or "Subject" in the list view of messages (at least in "Classic Layout" mode).

Sometimes a corrupted message can actually screw up the interaction between Mail and the server, even if message is corrupted not on Mac, but on the server itself! (seen happen w/ AOL).