Do you have any bundles installed? Look in ~/Library/Mail/Bundles (i.e. your user folder) for 3rd party mail extensions that may have been rendered incompatible following a system update ... I had symptoms similar to that once, and the culprit was an outdated version of Mail Tags.
Otherwise try moving (e.g. to desktop) the mail preferences files in ~/Library/Preferences ... if that doesn't fix it, just move it back. When Mail realises the pref files are missing it will create new ones without your account details, these can be safely replaced with the ones you moved. Close Mail first, obviously.