I am sorry to hear you are having problems but let me help you with that.
Can you please provide the CIR model you are using? Can you please provide the NUC model?
Thanks for helping me out ..
I have the latest D54250WYK which has the infrared receiver biult in.
I have installed windows 8.1 and am using the CIR drivers for the NUC downloaded form Intel website.
I checked device manager, and it is showing two entries in HID section:
Microsoft eHome Infrared Transceiver
Nuvoton Consumer Infrared
More than likely, the Xbox remote does not support the RC6 IR protocol, which is required by the NUC. Look for that in the specs for your remote. Here's a link to some reviews of RC6 remotes: http://wiki.xbmc.org/index.php?title=Remote_control_reviews
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I'm using a generic Lenovo branded MCE remote, and also the MCE remote that came with an old Linksys media extender, and they both work fine with my NUCs.