The MP4 files that you are not able to play, are you able to see those files on the TV? If yes, updating twonky wont make any difference since the files are being served to the TV and the TV is not able to handle the files.
Check if you have any updates available for your TV.
See if the following link helps
http://community.wd.com/t5/My-Book-Live/update-twonkyserver/m-p/119792/highlight/true#M441
