I believe the problem has something to do with having a non-matching sf2 bank when compared to what the midi itself is using. I'm currently using the TimGM6mb.sf2 set on default. I have this problem with a good deal of midi files, but not with ones I have exported from Musescore 1. I think this is because I am using the same soundfont as Musescore 1 is using. Anyhow, here's a link to a midi that is giving me problems:
https://drive.google.com/open?id=0B_5S_ ... GJNU3MyVnM
https://drive.google.com/open?id=0B_5S_ ... GJNU3MyVnM