Resolved: Joystick Support
 

When I enabled the Joystick support my character started running to the left. So I disabled Directinput and it seemed to have fixed it, Until I tried to walk. When I pushed left on the joystick he went right. When I pushed right he went left. The setting in the controls were right, I had to set left to Joy_Right, and right to Joy_left to move properly. :-/

Sounds like your joystick needs to be remapped.