I suspect that your problem has to do with a misbehaving CODEC. If you construct a similar scenario in WiMP (Windows Media Player), including using a playlist and playing several files in sucession, do you get the same result?
Do you notice that it is certain MPEGs and not others (can you test this out)? What type of MPEG files are they that misbehave? MPEG-1, MPEG-2, or MPEG-4? Are these the VOB files you mentioned in your other post? And what codec is your system using to render the file? Do you have any weird or specialty codec's installed on your system (Angelpotion or anything like that)?
If you don't know what codecs you have, get the G-Spot Codec information tool (which is here
http://gspot.headbands.com/) and use it to tell me. You should also know that it is definately not everyone who has this problem, I've never seen that!
BTW, this is irrelevant to the discussion, but I wouldn't say necessarily that 200 MB mpeg files are large (since most video files would be larger than that really).