How did you repair permissions? Disk Utility? That won't do it on user files, which might include the stuff you're having problems with.
You might try resetting to defaults if you haven't already.
If you deleted the account from Mail Preferences, restore the <home folder>/Library/Preferences/com.apple.Mail.plist file.
Then try the special handling for Mail and Time Machine backups. See the blue box in Time Machine - Frequently Asked Question #15.