This posting is older than 6 months and can contain outdated information.
Thanks for posting your results.
1) No firmware updates have ever been issued by Apple for the Apple IR Receiver that it puts into Macs.
OS X Mountain Lion, Remote Buddy and Candelair do not perform any firmware updates.
2) Apple changed both the sleep behaviour (in general) and wakeup reaction (to many peripherals, including mice and the Apple Remote) in OS X Lion already. For details, please see:
http://www.iospirit.com/blog/article/157/Waking-the-sleeping-Lion-Remote-Buddy-1-18-1/
http://www.iospirit.com/labs/candelair/releasenotes/ (Version 1.7)
3) Please see System Preferences > Security > More options (bottom-right corner) and check that OS X hasn't disabled your IR Receiver (which is the default OS X setting).
Based on your reports, the only explanation for your Mac not reacting to presses on your Apple Remote is that your Apple Remote needs a new battery. When the battery level is low, the Apple Remote will first send a "low battery" signal with every button press, and only then the actual button press. I can imagine that, with a very low battery level, it may only have enough power to send the "low battery" signal. Since it's a valid Apple Remote IR code, it'll wake up a Mac, but - since it's not a button press - won't trigger any reaction.
Best regards,
Felix Schwarz
