Same here. MacBook Pro 15" with Retina Display.
Tried repairing security permissions - no change.
Tried rebuilding mail by deleting the envelope files as follows, but no change:
"You can rebuild the Envelope-Index by throwing it away, it's located at ~/Library/Mail/V2/MailData/
1.Your Library folder is hidden by default. Select Finder (in the dock) > “Go to Folder” and then enter “~/Library.”
2.In ~/Library/Mail/V2/MailData, delete any file that begins with “Envelope Index,” such as Envelope Index or Envelope Index-shm.
3.Mail will rebuild the Envelope index when it is reopened. It will take a few minutes to rebuild the entire index."
I have multiple accounts, so I went into Mail, Preferences, Accounts and disabled all but one account to try and isolate it. This then worked OK.
So I re-enabled one account at a time and each time checked whether it worked. One by one they were re-enabled and worked OK.
In the end I had re-enabled all of the accounts that I disabled, and it was working. Can't explain it.