You cannot change how MP4 is handled by the xbox but there is a solution.
All you need to do is change the MP4's into MKV's. There is a very simple way to do this.
On my
Tools page is a software called Metafox. It can process a single file, or an entire folder.
Just drag n drop your mp4 to the installed Metafox desktop icon - it begins processing immediately.
It can use almost any file as the source.
It extracts the audio/video components and places them. untouched, into an MKV.
Here is instruction on how to get proper playback of the MKV file on the Xbox360