I have the same problem. I've verified that the CIR is on and it shows in the device manager. Then I set up both IRSS and eventghost, and neither seem to pick up any signals from my apple remote, even though according to the internet, it should work.
After investigating the issue myself here is what I figured out.
Intel nuc supports a certified Media Center Infrared Remote Control.
This basically means a RC6 protocol remote is required.
After saying that, Media Center remotes come in (as I see) 2 types:
1. Certified (RC6 explained above)
2. Other proprietary protocols
The 2nd type MUST come with an IR receiver which translates the remote's buttons commands to keyboard\mouse keystrokes\clicks and movement.
So, if you want a remote which is compatible to nuc`s receiver the solution is to buy a certified Media Center remote.
Finally, as a nuc owner myself I ordered the following remote because it is certified (RC6), has backlight, programmable to control other devices and is fairly cheap:
Inteset’s INT-413 Media Center Infrared Remote Control (without the IR receiver is priced $16.95).
I use it with XBMC with no problem.
Hope it helps!
Did you look into the option of using Eventghost or IRSS?