Make sure the controller is wired correctly to the turnout.
Test the turnout by disconnecting it from the track, and disconnecting the controller. Apply power to the center and a running rail of the turnout. Take a screwdriver and short the center terminal of the turnout to the left terminal, and then short the center terminal to the right terminal. The turnout should throw in both directions. If it does not, there is an internal problem with the turnout.
See here for a wiring view,
http://pictures.olsenstoy.com/cd/swt/stc022a.pdfand here for a phantom view of the turnouts.
http://pictures.olsenstoy.com/cd/swt/stc022c.pdfThis should help you trace the wiring for proper hookup and operation.
Larry