now that doesn't look too good. The System Preferences Pane goes 
through a private Apple Framework to check for the Apple Remote's 
availability and adjusts its UI accordingly. The Framework itself 
checks for Apple's "AppleIRController" kernel extension (you can 
easily check whether it was loaded by your install on startup - and 
it should - by entering

kextstat | grep AppleIRController

in Terminal. You should get something like this in return:

75 0 0x761000 0x4000 0x3000 
com.apple.driver.AppleIRController (55) <74 37 19 11>

If not, Apple's IR driver was not loaded automagically by OS X on 
startup.

Then, to exclude the possibility of a hardware failure, please check 
your System Profiler's USB information for an "IR receiver" device 
with this info (sorry, the words of mine is all in German, but the 
technical data should be the same):

Version: 1.07 
Bus-Strom (mA): 500 
Geschwindigkeit: Bis zu 12 MBit/s 
Hersteller: Apple Computer, Inc. 
Produkt-ID: 0x8240 
Hersteller-ID: 0x05ac (Apple Computer, Inc.)

If you don't get any info there either, this is most certainly a 
hardware problem. Even with totally defunct IR drivers, the IR 
receiver would still have to enumerate on the USB bus and turn up in 
System Profiler.

You can, btw, also reset pairing and any "IR receiver disabled" 
setting by deleting

/Library/Preferences/com.apple.driver.AppleIRController.plist

and rebooting.

Please also check you have the AppleIRController driver in place at

/System/Library/Extensions/AppleIRController.kext

Please also check you did neither move, corrupt or delete this file 
(which, btw, would require root priviledges and thus can't usually 
happen without your explicit permission and decision).

If you want absolute certainty whether this is a problem with your OS 
X install or your hardware, make a fresh OS X install on a spare 
external harddrive (or boot off of your mate's MacOS X install using 
the Firewire target mode and a Firewire cable - search for it on 
Apple's support pages for explainations and how-tos) and check 
whether the problem persists (=> likely a hardware defect then) or 
this solves it (=> likely a software problem then).

However - and I can't stress this enough - Remote Buddy carries 
neither any code nor does it ever run with the necessary rights to 
make any changes to your system install or change, terminate or 
affect the default behaviour of your Apple Remote in any way. It's a 
completely passive solution and you can grab the driver sourcecode in 
use from www.martinkahr.com.

The information I've supplied you with in this thread is all I can 
offer to you. I hope it is of help to you. Beyond that point, only 
Apple can help you further as they've both designed the hard- and 
software that is giving you problems here.

Best luck and best regards, 
Felix