I know my controller requires getting a signal from the line which runs off the brake pedal switch. If your controller requires this, have you checked to see if this connection is proper? If your controller cannot detect the change of the state of this switch, your controller will not send power to the brakes.
When you are in a manual mode that connection is not needed. Have you attempted to manually activate the brakes without stepping on the brake pedal? If they engage I would believe that the issue would be that wire to the brake pedal switch or line.
'04 Classic 30' S.O.,'03 GMC Savana 2500,'14 Honda CTX 700