As I work with this, part of the issue appears to be mixing and matching of remote control devices and the protocols found in the Remote Devices in Cubase. The MCU PRO sets up with the expected functions with the Mackie protocol. It appears a conflict arose when I added my Sonar VS-100 audiointerface as a remote control device as well. Really, the only thing I wanted the VS-100 as a remote was for the foot pedal which can start/stop/play and record keeping my hands free for piano or guitar playing. When I added the VS-100 as a Mackie remote, it screwed up the MCU PRO’s track functions. When I deleted the VS-100 as a remote control surface, the problems with the MCU disappeared!
So, I then configured the VS-100 as a ‘generic’ remote. Basically starting from zero settings. The ‘learn’ function makes this easy, so I quickly set up the VS-100’s transport buttons. Now the foot pedal works fine with the intended functions, and the MCU PRO doesn’t get confused over incoming signals. I will further tweak the VS-100, but I don’t really need this for the track controls at all, just Transport functions.
It would be interesting to see what confusing messages were being sent by the VS-100 to the MCU PRO, but right now it isn’t that interesting.
So for now, the issue I was having has been worked around.