This is a general problem in the MCE which should be corrected in the next update (said to be coming soon).
As a possible workaround, disabling a track will prevent it being represented on the controller - this may or may not be acceptable in your case.
I seem to remember that if you create a Folder, and place the tracks to be hidden in that folder, and turn the visibility for the folder off (possibly as well as the tracks themselves) that this will work too. I can’t verify this ATM however.