Generally sounds like some sort of preferences issue to me. (Create a test user if you don't have one, add an E-Mail account to Mail.app and see whether the problem appears there, too.) If, as I suspect, the test user would be fine, I'd go about removing preference files for Mail.app. The most obvious one is ~/Library/Preferences/com.apple.mail.plist – I'm not sure what is all contained in this one file. Make sure to make a backup before deleting files.