No, it does not work outside of Kodi. I tried Notepad with no success. It works fine with the GUI; I can record remote commands.
I have tried uninstalling (through device manager) and reinstalling several times with no luck. I also tried the procedure with Zadig. I noticed that it lists flirc twice; once on Interface 0 and once on Interface 1. If I uninstall via device manager, I can uninstall. But when I reinstall, I always get two that show up. Not sure if this is typical or not.
One observation I will make is that the GUI always defaults to the Minimalist Controller. Is it supposed to work that way if I select the KODI controller?