I experienced the same issue; after a while the IR stops responding to any command my harmony sends.
As a work around I plugged in a FLIRC(gen2) for Kodi navigation and only use the NUC's IR for the 'Power On' functionality (from complete powered off state). And I need to remap a button so that the FLIRC can power down the NUC.
NUC7C, Ubuntu 18.04
Thanks for the feedback. User keoma pointed out yesterday over at Kodi forums that downgrading the BIOS to 0027 solved the CIR issue on the NUC7PJYH. I have confirmed that solution (workaround, rather) today for the NUC7CJYH. Will update my initial post accordingly.