I find half a dozen different "MusicTime" thingies on the web, but I presume you're talking about the gVox music notation/midi program. If that's the right one, I don't see anything obvious that should be upsetting your setup, but one never knows without hands-on in-depth probing. I've had difficulty getting midi device settings to do what I expect, with a similar notation program; but the problems I've seen have never affected anything but the program I was trying to get the keyboard to feed into, and only while that program was running.