Got the same problem with my X52 pro. Makes the game unplayable because as soon as you enter a mission you start accelerating in one way and there doesn't seem to be much you can do about it.
I've tried setting huge deadzones for the precision slider and the rotaries on the throttle, but that doesn't seem to do much really as the lateral thrusters get fired randomly by just using the throttle itself.
Also the game seems to be stuck in free mode for the thrusters, as it ignores whatever speed you set with the '+' or '-' key, and pressing 'n' to switch to assisted mode doesn't work, even though the icon for this in the cockpit does change.
Switching the controls to keyboard in the game options also doesn't help, as apparently this only disables input from the x, y and z axis from the stick, but leaves the throttle fully enabled and as such still leaves you with wonky lateral thrusters.
So far the only option I've found that makes the game playable for me is to completely remove the joystick in windows itself. Seems that as long as the game detects the joystick it just refuses to let you control anything thruster-related with the standard keyboard controls.
Really weird stuff.
Shadowcat: Have a look at psg\resource\keybind.ini
I've not played with it myself, but it may facilitate the changes you need.
That only has the keyboard bindings as far as I can see. The joystick binds appear to be hardcoded.