It sounds to me very much like a Sysex problem. What some people are unaware of is that midi files will play on many different keyboards and modules, but will not play or will do all sorts of unpredictable things on others. This is why I think you get the problem on some files and not others. The problem files may need a GM/GS reset sysex command (which is set automatically at the beginning of the midi file). It's good policy to always do this anyway on all your midi files, especially those off the net.
Hope this helps.
Ron