I had a weird Apple TV menu button issue with a C4 system. The Apple TV refused to respond the IR menu command, even though the indicator light on the front of the Apple TV would blink, and all the other buttons seemed to work. Not only that, but another Apple TV in the system (same model) was working fine on the same driver.

Another C4 dealer told me to delete any "learned remotes" in the Apple TV settings. That fixed it. Not sure how since I never set up a learned remote....