During my initial session, I was able to game using my Logitech F310 gamepad with no problem. Every time I try to start the game up again, however, the controller input goes to hell. The game recognizes that a controller is there, but A is reassigned to B, the camera is now controlled by the two triggers instead of the right control stick... you get the idea. Remapping the keys in game does no good, as the game simply refuses to recognize that certain buttons exist. I've tested the gamepad with other games, and it appears that this is the only game that it is having problems with. Is there some way to fix this, or is AC just fucked for this controller?

I feel silly in hindsight. Turns out on my initial playthrough I started the game while the controller was in DirectInput mode and on my subsequent playthroughs the controller was in XInput mode. I had thought I could rule out incorrect input mode being the problem, since I toggled it in game, but it turns out that input is only checked on initially starting the game up; toggling input modes after that just turns the controller off and on.