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ekj7: I have 2 360 wireless controllers, but neither of them seem to work when it comes to calibrating the controls. The red up-arrow appears, but when I hit up on the pad, nothing happens. This occurs for any of the controls and all I can do is hit space to skip them, or ESC to exit. Needless to say, the joystick doesn't do anything in-game either.

Both joysticks work fine in other games.
When you're calibrating the controller, don't just press whatever button/stick once but hold it until the direction arrow turns green then move on to the next one. Hope that helps :D
ekj7: Held the direction pad for over a minute, still doesn't detect it.
Weird. I just downloaded and installed the latest version of the game on the site (1.43.3) and ran the controller calibration utility in the game and then proceeded to finish off a quest. Everything seemed to work fine. Have you checked your controller's drivers perhaps? Tried a different USB port?