[Bellerophon]

If the battery is too low charged it should just activate low voltage protection and not go into programming mode (that is, for the expected battery type, ie a fully charged 7.4V lipo will trigger low voltage protection if the mosfet's set to accept an 11.1V lipo).
Normally it'll only go to programming mode if the motor's disconnected, either because of a physical breakage of the wire or because a short circuit lets the current bypass the motor.

Sorry if it sounds obvious, but are you sure you wired all the connectors to the correct polarity? If the opposite polarity if applied to the motor, it'll spin in reverse, hit the anti-reversal latch, and stall; at stall the mosfet will see a short and disconnect itself.