Controller setup issues

I had the game running fine using my 360 controller, loaded the game into steam to try over steam link and now I am having issues. The controller keys are working like some unknown keyboard controls. for instance the left analog stick is working like Q,E,Z,C and B is working like SPACE. Not sure where to go here is what I have done so far.

1) removed from steam
2) deleted local config file
3) reset configs in game
4) uninstalled and reinstalled
5) system config/gamepad settings/enable gamepad set
6) system config/gamepad settings/button configuration setup
7) if I try to do the calibration it gets messed up because it registers the commands as in game buttons so it cancels etc. Like its not registering it as a gamepad but as keyboard controls. It does however how the buttons being pressed.
8) keybind/gamepad doesn't have anything configured. Not sure if this is suppose to be set, it is registering buttons, just keyboard buttons. If that is suppose to be filled out can someone send me what its suppose to be set as? I hit default and it left it blank.