I use the Mackie Universal Pro. I have it hooked up with MIDI cables, as I had issues using it with USB. I notice that frequently when a song first loads or I start up Cubase, initially Cubase doesn’t respond … even though in the LCD on the unit it knows it’s talking to Cubase.
Usually if I hit the transport control with the mouse once or twice and then hit the same function on the controller, everything works fine until the sessioin is over.
If the glitches you are having are similar, that is, just happens once and then everything is OK, maybe its a Cubase thing. On the other hand, if it crops up repeatedly, maybe it’s the unit. Those HUI’s are getting pretty long in the tooth.
Try disconnecting the motors from the fader and see how well it works.