First thing, make sure to update to the current build. I don't think you are right now because...
The current build should re-analyze files on manual import, so you shouldn't get the "previously determined to be bad" message anymore when you do the Run Auto Import Now.
Also, just to check, is Options > Video > Video Mode set to Red October Standard or ROHQ, or some custom mode? If it is custom or HQ, try switching to ROST to see if it is a custom setting (or some problem with HQ mode). Lastly, check the settings for MP4 under Options > File Types and make sure the Playback Method is set to Automatic.