I was messing around with the THR_MIN parameter today and set it to 5%. It appeared to work as expected, in manual mode the motor did not spin when I had the RC radio throttle stick at 0%, when I switched to FBWA the motor spooled up to 5%, this was unexpected because I thought FBWA used manual throttle input, but I assume this is because it is using all the limits set for automatic flight modes.
The thing that really does not make sense is that when I disarmed the plane the motor also went to 5% and the only way to get it to stop was to re-arm the plane and put in manual mode with 0 throttle input on the RC radio.
It appears the MIN_THR parameter sets the disarmed throttle output. I think this is a very dangerous thing to do, if the plane is disarmed there should be no way to send a throttle value other than 0% to the speed controller and I want to see if anyone has an explanation for why this is the case or did I just find a bug in the code.
If you disarm your plane, the PWM output should be 0. You may verify if this applies to your plane carefully with the propellers removed.
You may also ask on Ardupilot forum for better support about your parameter settings.