Jackedman,

The only thing that comes to mind is maybe the new motor is pulling more current and is overheating the FET that drives the motor. Does the EM400 seem to be more powerful than the stock motor? If this is indeed the case, you might be able to solve the problem by using some thermal epoxy to attach a heat sink to the FET. There could be other reasons for the problem, but that's all I can think of at the moment. Also, are you using a pinion with the same number of teeth on it as the stock motor had? Are you sure the gear mesh isn't too tight?