In what order are you connecting the controller? If you refer to the manual, you must connect the pump and controller first before you connect the pump to power. If you have the power supply connected to power and then connect the controller and then the pump, the controller will flash a red light. You must connect everything first before connecting the power supply to the wall.
Also, how did you find out that the issue was in fact the controller and it needed replacing? Did you test the motor block to make sure that the problem was not the motor block instead?