I am having the same exact problem you are having. This all started when I installed Mountain Lion on my Mac Pro. None of my iMacs nor my MacBook are having this problem. I reinstalled Mountain Lion on my MBPro last week, but the issue persists. It's very, very frustrating to me. Have you learned of anything else we can try to fix this problem?
Thank you JadedEye. Your solution worked for me today. A real lifesaver!
Message was edited by: usermac added reference to JadedEye for clarity.
Miraculously, the post below about Lion works for Mountain Lion as well.
This same thing happened today when migrating a friend's laptop.
Inside the Library folder (Lion hides this folder now, so hold down the option key and use the Go menu in the finder — Library will appear in the menu. Go there.) you'll find the Mail folder. Inside the mail folder was another folder called V2. I simply took the contents of V2 and dragged them to the parent folder (Mail).
When I launched mail again, everything was back to normal. As Apple says, "It's that simple!"