Mary,
While I have never played with your specific software, what I can say is that almost all midi files have system info at the very front of them....things that tell the keyboard how to play etc. It could be that this info is confusing your software because it does not understand these "system commands."

What you can try is this...if you can edit these midi files with the software, then go to the very beginnings of them and look at what is there, if you see a string of stuff on one or more tracks, try deleting just this front part.

Terry