One thing to try is this:
Quit Mail if it's open.
Go to your Library folder (click the "home" icon in the sidebar on a Finder window, open up the Library folder there).
Find the Mail folder. Create a safe copy of it first by right-clicking on it, then selecting "Create Archive of 'Mail'". This will create Mail.zip, which contains all of your mail.
Now that it's safe, rename your Mail folder to Mail2 (or anything different than "Mail").
Restart Mail.
Let it load the mail it knows about.
Go to File->"Import Mailboxes", choose "Mail for Mac OS X", then choose that folder you renamed.
This should fix things.
If not, quit Mail, delete the Mail folder, and unzip the Mail.zip file.