Yellow Dog Linux

I have spent a lot of time converting MKV's to other formats so I can play them on my PS3 and I have noticed that non MKV formatted files seem to be easier to decode on my PC. When I say "convert" really I more so mean re-mux because I set mencoder to simply copy the audio and video codecs into a new container (usually MP4) and so I must conclude that MKV's are for some reason more difficult to decode.

Does anyone have any information that would support of contradict my findings?