I'm not a MAC user, but ---

Are you just listening to these MIDI's off web sites, or are they MIDI's that you produced or imported into your own music software?

If you can see the music, are the bar lines lined up as you look up and down from one staff to another? If not, then there is a note or a rest which is missing, extra, or not the right length for the measure. Find it and fix it.

If your melody has pick-up note(s), are there rests of the same length in the staffs below?

I have another thought, which is a little vague, but here goes. I have found that MIDI software does not handle pick-up notes well. Actually, it doesn't believe in the existence of pick-up notes and tries to incorporate them into the first complete measure of the song. After that, all the bar lines are in the wrong place. This could be a factor. (I'm speaking here of situations where you download a MIDI from a site into your music software.)