The square wave disappears and is replaced by a constant battery voltage that lasts for a few seconds then most of the times drops down to about 9 volts (with no cogging) sometimes it goes down to about 0. I've had a few times where it seems like everything is fine (almost no voltage on phases) but the motor still cogs, which is "fixed" by applying a small throttle (just enough for the PWM to start) and then waiting for the remaining battery voltage to disappear.That's OK. So you can check the signal between GND and the three phase wires first. There should be no signal, if the motor has been in standstill for several seconds. If you turn the throttle slightly, there should be a square wave with an amplitude of the battery voltage with a duty cycle of about 50% on all three phases.
May this have anything to do with the "dead resets" and no response to throttle input with a constant speed after the initial spin up?