According to the data found in the source code, Movie Monkey supports the following formats:
'avi', 'divx', 'flv','mkv', 'mov', 'mp4', 'mpeg', 'mpg', 'swf', 'wmv', 'x264', 'xvid'
If you have files with extension other than the ones above, they won't be added to the database.
Also, install the latest version from the official website: http://getmoviemonkey.com/