I had an issue pairing my Apple Remote with my MacBook Pro. The Apple manual says (on page 36):
To pair your Apple Remote with your MacBook Pro:After trying and failing several times to pair my remote using these instructions, I gave up. While it could be a bit annoying not to have the remote paired, it was not a significant enough issue to prompt me to send the notebook in for repair. After a few days, I decided that there must be a software conflict causing this problem, since the remote works fine otherwise. I scoured the net for a solution and found nothing. It seemed I was the only one with this problem.
- Position the Apple Remote 3 to 4 inches from the IR receiver on your MacBook Pro.
- Press and hold the Menu and Next/Fast-forward buttons on the Apple Remote for 5 seconds.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060308130231850