@WebMaximus I use minimal Ubuntu with XBMC installed. This is essentially the same as XBMCBuntu. As stated it my Harmony works. You may want to check the XBMC forums and Wiki on how to configure a remote. At the very least you need to check the system and XBMC logs to see if the driver is correctly loaded and detected by XBMC.
@Gumbo_K Although this NUC doesn't seem to be Linux "friendly", Linux does work. I have the same 'Firmware Bug' in my dmesg output and I am able to successfully use the CIR and shutdown. So not sure what you mean when you say you can't shutdown. As for question regarding if you should return it, depending on your technical level and patience you may want to. However, you can get the NUC working with Linux and CIR. At least on Ubuntu 13.10. But I don't see why other distros and Ubuntu versions wouldn't work.
For both of you... There is a workaround for the specific issue described by the OP.