Well, I feel a little silly, but I figured it out. The issue persists with my xbox controller, but I figured out why the ps3 controller wasn't wanting to work. I had the p1 controller set to default like the rest of them, which defaulted to the xbox controller which only worked when I replugged it in.
When I set p1 controller to the ps3 and p2 to the xbox, things are working well enough. The ps3 controller works in games, but the xbox controller still needs to be replugged (I may not use it much from now on anyway)