Considering that generic remotes don’t recall correctly (i.e. by default rather than xml auto-import), I would say it’s a bug with something in the CMC controller config that isn’t activated after a restart.
What you are seeing may actually be there with any controller, but since most are simply midi CC controls, it may not affect those - i.e., you move a cc control, and Cubase sees the assignment.
The CMC may have additional sysex or midi messaging that has to be reset before Cubase can see it’s assignments.