So, after I posted, and after we talked on TS, I started noticing major problems.
TS does not play well with CH stuff at all.
So, after reading the TS forums, it seemed like the problem was stemming from the Gampad and Joystick Support Plugin (added to TS 3.1.1).
I have no idea what this does, as I don't need hotkey support from TS.
So I went to Tools > Options > Addons. And uninstalled it.
Now everything works fine.