Thank you for your response. Mission planner is actually able to arm perfectly fine when I have the motor connected to RC channel 3 the motors beep and arm. Mission planner also allows me to arm perfectly fine. I make sure as well to set the flight mode to Qstabilize. However, when I connect my quad motors to channels 5-8, the motors only do the first initial beep but does not give the "initialized" beep. In mission planner (with Qstabilize set) I am able to Arm as well but motors are not spinning (since they are now coming out of channels 5-8). It's like you are getting a pulse to initialize the motors only in channel 3.
I tried one more thing to ensure it is not my board: I initialized the motors in Channel 3 (it worked fine). I then changed the esc cables to channel 5-8 and it works. There seems to be a setting somewhere in the parameters that can set the quadmotor channels to initialize the esc as well (as channel 3 does).
I hope that made sense. Reading through the internet, it seems several people out there are having the same issue. Since APM Plane defaults to fixed wing mode, it only gives the channel 3 the ability to initialize the motors/esc.