I am using a Harmony IR remote (the 650) and have the Flirc set up using the Kodi profile. I programmed the Home button in Flirc as it wasn't working correctly in Playstation Vue. All basic functions work properly now EXCEPT on some apps, like Fan TV for example, the "select/OK" button does not work yet it works in most every other place. The spouse acceptance factor is suffering!
I saw you posted the issue on the FLIRC forum as well. I hope someone comes up with an answer as I just got the Shield and HBO GO/STARZ won't work with the OK button. Every other app seems to work fine.