Method of operating an electronically controlled throttle controller between two modes of operation, including a transition between modes, includes powering up an electronics package and determining if a short term power out, a long term power out or a loss of CPU control in either short term or long term has occurred. The position of throttle, dynamic brake and reverser handles is compared with a previous mode of operation to determine current mode of operation. If it is determined that the throttle controller is in handle mode, the output signal to the trainlines is adjusted according to handle positions. Outputs of throttle, dynamic brake and reverser handles are set in the home position if an RMU command is received. A predetermined delay is imposed when outputs of the throttle, dynamic brake and reverser handles are in home position after positioning by an operator of the locomotive and before exiting a handle mode and entering an RMU mode of operation. If an RMU command is received by the throttle controller after the controller has exited from handle mode, then the output signals are adjusted to the trainlines.