I have notice this problem as well. I have figured out how to fix this to convert all my DVDs over to MP4 that will play on WiiMC.
Basically, a standard DVD has a default resolution of 720 X 480
Reducing the resolution down to something like 640 X 368 seems to fix this problem. I am not sure why.
I do this using HandBrake. But it is a pain to convert over all these MP4 over using this method. It would be much easier if this MP4 problem could just be fixed.
I hope this helps. If everyone wishes, I can put up a guide that will give everyone step by step instructions on how to convert their DVD libraries over to MP4 so they can play it on WiiMC. It might be useful to some people. That is exactly what I have already done and for years now my TV does not play any discs, just video files. I got rid of my DVD player and just have a Wii and Media player hooked up to my TV. I would get rid of the Media player if this problem would get fixed.