Yeah I have had that problem switching midis to new (After Window 95) computers. I think it relates to the tracks "forgetting" what instrument sound they were supposed to make and substituting a new one. Or just different codexes assigning different instrument sounds.
What I've found has helped for me, though it's tedious, is to use a MIDI editor to manually "fix" the song. I did this mostly with MIDIs I myself had created.
I forget what program I used, but just google "freeware midi editor".