I use Music Creator 5 in Windows 7.
 
I am using Music Creator 5 to create midi files for our organ at church.  There are three tracks I need to set in order for the organ to play correctly.  The three tracks go to the MAN I keyboard, MAN II keyboard and Pedals.  Everything works exactly as I want as long as I use all three tracks.  However, if I only want to use two of the tracks, I have problems.  I need to keep the volume setting for the track I don't use, but I don't want any notes played.  I noticed that my problems go away if the track I don't want to use has no notes and is muted.  The problem is, I can't figure out why I can mute the unwanted track in some of my files, but not in others.  I toggelled from the automated mute to manual mute and that doesn't help.  I must have something checked somewhere to make the two files different.
 
I also notice that on some tracks the volume stays set to the way I set it and some of them go back to a volume of 101 after I save.

I, for one, need more details on exactly what you are doing, how it's hooked up/wired, and other important details such as the midi channel settings on the tracks and the controllers.  Are the 3 tracks all in one song or are they 3 separate songs?
 
I'm thinking/assuming... (and I might be wrong) that you send the midi out of the computer on a midi cable to the keyboards (3 total?) Each set to a different midi address/channel. At least that's how I would attempt to do live midi.
 
Sounds like you are using live midi controllers to do the live music. While it can be done that way, I would suggest burning CD's of the music and play it that way.... it's easier and there are no goof ups and glitches due to settings being wrong.
 
I saw a band once upon a time, in the early days of Midi using cakewalk when it was a sequencer for midi..... quite the complicated setup. It worked well.... but it looked like a nightmare with all the gear and cables and such.