Hello Mattias, we have seen this issue before and we duplicated it in our labs. We were able to use this feature without problems.
We used an RC6 remote control. We installed the driver, restarted the system and then, CIR was working perfectly.
I would recommend you to check if you are using the correct driver.
If you continue having issues, you can contact our warranty department so they can help you to replace your NUC since it could be defective. http://www.intel.com/p/en_US/support/contactsupport