I have a universal remote that has the Red/Yellow/Green/Blue bottons, and I have this exact issue whenever I have the remote programmed to a device that utilizes these four buttons.
I am able to program the Flirc receiver with ease when I have the remote programmed to a device that doesn't use these buttons.
This didn't happen in older versions of the firmware, but happens on all of the more recent versions.
I believe version 2.6 was the last version I was able to use, but I can't find the download for that anymore.
It's very annoying because I like to program these buttons to do certain tasks in Kodi, such as Subtitle On/Off, Audio Delay, Watched Toggle, etc...