If I engage the kill switch it should kill the motors and servo's. In some scenarios to prevent harm to people and the aircraft, having the ability to stop actuating the servo's at the flick of a switch seems important. I'm using a custom VTOL platform. Both MC and FW mode act the same. Also, at power up it seems very unnecessary for the pixhawk to command all servo's to their extremes.
Thanks for the advice though. I'll try changing the PWM Unarm length and seeing if I get any different results.