Well, ok, I create all my midi files using guitar pro 4. Now that I've updated a created a single midi file using guitar pro 5. When I play the midi file, the next music (if it's a midi) it will play weird, really weird, like the file is corrupted. However if you play the midi files externally they have no problem, if you also don't play the midi file created with Guitar Pro 5, all seem to work just fine. I think you should have a check on that. just create a midi file using gp4 and then one using gp5.
To start with, I think probably not everyone has GP4 or GP4 to test that :P. You better upload some example MIDIs.
I think it's a MIDI reset thingie. Often times if you play a MIDI after another and the device is not properly reset you may have this problem. Try to experiment with stopping the first MIDI before playing the second one and see if that happens. Some sequencers automatically insert initialisation codes to the beginning of a MIDI file so the device will be properly reset when you start playing it. I guess GP5 might have skipped that part under default setting, try to see if there are similar functi0ons.
Ok, sorry for not being much of help, despite asking the same amount by you guys. I'll try that and tell you.