The IR Receiver USB device is used by XBMC (PID 6316) 
An application is accessing the IR Receiver USB device via an IOUSBDeviceUserClient. Depending on what it is doing, this may keep OS X and applications from receiving Apple® Remote button presses. The application is located at /Applications/XBMC.app/Contents/MacOS/XBMC. 
Checking running applications 
EyeTV (PID 5675) is using the Apple® Remote in exclusive mode 
While EyeTV accesses your Apple® IR Receiver exclusively, no other application or OS X will receive Apple® Remote button press events. This can give you the impression that your Apple® Remote doesn't work. In that case, quit EyeTV (located at /Applications/• Video/EyeTV.app). 
XBMC (PID 6316) is using the Apple® Remote 
If XBMC is accessing your Apple® IR Receiver exclusively, no other application or OS X will receive Apple® Remote button press events for as long as the exclusive access is taking place. This can give you the impression that your Apple® Remote doesn't work. In that case, try quitting XBMC (located at /Applications/XBMC.app) and check whether it makes a difference. 
Testing exclusive access 
Can't get exclusive access 
RCD's attempt to get temporary, exclusive access failed (error: The operation couldn’t be completed. (Mach error -536870203 - (iokit/common) exclusive access and device already open) (3)). This usually means that another application is already having exclusive access to the Apple® Remote. Neither OS X nor other applications will be able to respond to your Apple® Remote at the same time. This can give you the impression that your Apple® Remote doesn't work. Quit the application that exclusively accesses the Apple® Remote to make it available to OS X and other applications again.

Yes, EyeTV is running, and I didn't start it. I'll try to figure out why EyeTV is self-starting, determine if that's the issue, and then report back. Although interesting that RB still runs in the Finder but not XBMC. Stay tuned...