If I hit my mode button, or don't set my controller to X instead of D, the same things happen to me.
Can you elaborate on this a bit? I'm not quite sure what you mean and if this is a fix for the problem I'm having. I actually found the bindings for the gamepad but it's kind of useless and doesn't let you unbind or give much freedom. Each button has a preset list of commands you can assign to it. It's in system configuration, gamepad, then Button Configuration =/
My gamepad has different modes you can activate, and if I hit the mode button located under the select button, it allows for input sequences to be set for a single keypress. If I'm not paying attention and that little light is on, it messes up all of my keybinds.
On the back of my controller, there is a switch and two letters, D and X. I can't remember what they stand for immediately, but they are for different input methods for games. I believe X is for newer games, and D is older. If I have that switch on D, my gamepad has the same issues you seem to be having.
I believe under Menu -> System -> Character Options there is a gamepad/joystick configuration option where you can reset all of your binds and move them around. I'm not in game right now, but it is under one of the options in that menu. Failing all else, you should be able to bind whatever you want to whatever key you want. You can also recalibrate your controller, in case you mixed something up the first time around.
If none of those work, that's all I've got unfortunately. Good luck!