Thanks a lot.
Your method works but I had to add /D right after cd because my files were on a different drive.
However there is still one game for some reason that does not want to work correctly.
It's Guilty Gear Xrd Rev 2.
I have the code like this:
@echo off
cd /D "C:\Program Files (x86)\GUILTY GEAR Xrd REV 2\Binaries\Win32"
"BootGGXrd.exe"
Apparently with this game I have your original problem where the game launches but pressing on the controller starts controlling AM in the background (no focus on the game).
Also another weird bug I can't figure out is, if I kill the game (alt+F4) upon boot, it will return to AM but now AM's resolution is all messed up. Enabling ResFix nut does nothing too.
If anyone who reads this can chime in with some suggestions that would be great.
All in all, your batch tip has helped for the rest of my game list so thanks!