I like Shinta215’s hypothesis on this actually. Definitely makes sense and well thought out and reasoning I must add. Kudo’s for that! 
However, I used to have a BCR2000 and had set it up as both a generic remote and a Mackie Control device at the same time…so basicly the same scenario: two midi devices sharing one physical device, and had no issues.
Perhaps the CMC series use a different (longer) handshake than the BCR2000 did, or perhaps this behaviour has changed in newer Cubase versions? Either way, it’s pretty interesting to find out what is actually causing this now.
Just using the CMC’s as a generic device is no good for me either, because there are some functions I want as well that the CMC extension offers that I can’t set up via generic remote. Although I guess I could try it out for giggles to -perhaps- support Shinta215’s hypothesis. Nice thinking csd, I like your style! 
Thanks for the feedback guys…