I had the exact same problem: I have Mac Mini, all the remotes work, but I need to pair the remote, because I have Apple TV next to it, and the remotes must not interfere each other.
The pairing didn't work. The disabling and enabling IR didn't work. (I did not try to configure Kodi to disable remote, and then do the reboots and system preferences), many different key combinations didn't work..
BUT!
I had a program called USB Overdrive installed, and I remembered that people have issues with Openemu and joysticks, because it takes some kind of control of HID and other(?) API's or something.
==> I uninstalled the USB Overdrive, and everything works. Didn't need to touch Kodi's preferences at all.
So If someone uses USB Overdrive, watch out: your joysticks and remotes might not work like you wanted.. 😉