I've set up Soul Reaver with JoyToKey so I could use my Afterglow 360 controller, but I can't get it to work correctly. In game it works alright, however when I'm trying to navigate menus it's very very sensitive and the selection moves constantly. Movement in game also does feel slightly strange but not terribly broken. I don't have either joystick set to anything and the game is set to keyboard controls. Is this just a problem with Soul Reaver and JoyToKey, or 360 pads, since I'm not using Xpadder or a PS3 controller? I know the built in controller support in game doesn't work correctly with controllers with sticks but it shouldn't be using it at all.

Maybe is a problem with Joy2Key. I remember that you have to change the controls from gamepad to keyboard so Raziel can stop moving by himself, as it seems you did. It has been years, but this old post of mine explains that, with a profile for Xpadder with a Xbox 360 controller:

http://www.gog.com/forum/legacy_of_kain_series/gamepads/post11