Recently Apple has moved through multiple iterations of mail types. First it was .mac, then MobileMe, and now iCloud. Because of this, I would presume that sometime while updating, something went wrong with your email client and its connection to .mac. I have had this problem a few times before, and the way I usually fix it is by removing every trace of my email account and re-adding it.
- sign out of .mac in the correct pane under System Preferences
- go into Mail>Preferences>Accounts and remove your .mac account, and quit Mail.
- now re-add your account under System Preferences
If this doesn't work, I'd suggest simply cleaning out the Mail app and starting from scratch.
Sadly this is a little extensive, but fixing this annoying problem is worth it.