I've been having remote unpairing issues.... even after having numerous repairs, and furthermore, still having them after receiving a replacement Mac and remote.
I believe there is a flaw in the latest MBPs and iMacs, and nothing to do with the actual remotes, or the software, as I have tried my spare remote, and clean installs, and it still happens intermittently.
Heard of only 1 case of remote problems, which was a poster here with an iMac, and other than that, google led me nowhere, and my last MBP has Apple techs, going all the way up the chain, stumped.
In my last MBP, they changed the IR receiver and cables, and all the possible parts, and still no fix.
When the remote unpaired itself, my spare remote stopped working too, where as both remotes work with my MB booted off the clone of this MBP without any glitches.
I think remote issues will be something that starts rearing it's ugly head soon over the forums!
I actually added a third party software (driver) that I am testing called candelair to see if that makes a difference.