For reasons unknown, the Elite Series 2 controller is recognized as both an Xbox controller and a keyboard; a standard Xbox controller is not.
I had noted on my Xbox that if the sim recognized my controller first, before my keyboard, that my keyboard wouldn’t work.
I’m wondering if this is what is going on with your set up. I’d try something as simple as unplugging your keyboard and launching the sim with just your mouse and your Xbox controller and see if you are able to make those custom functions work.
When I switched to PC, I left my Series 2 to use with my Xbox and use the standard Xbox controller with the PC and don’t have any issues with it and my custom Xbox controller mappings.
Anyhow, start there. You could also try pairing the stock Xbox controller to the PC (leaving the Series 2 off) and see if that works, too. If you try this, don’t forget to quit and relaunch the sim, just to ensure the Series 2 is truly not a part of the situation.