The APM 2.5 is not for the faint heart.
I can't seem to get the yaw servo to operate when I move the rudder stick on transmitter while all motors are running. I have the servo connected per the APM wiki manual (http://code.google.com/p/arducopter/wiki/APM2_Motor_order). It is connected to port 7 of the outputs side of the APM board. The board is powered, using the APM power module. I also checked the radio controls via Mission Planner (Radio Calibration) and all the radio controls (roll, pitch, and yaw) appear to work as intended.
The postman delivered my APM 2.5 yesterday, Christmas eve. I was thinking to myself, it must be Christmas. ;)
So, I spent almost all Christmas eve setting it up, went to bed around 4am, trying to hook everything up. I didn't rush anything as I didn't want to screw up or fry anything like what I have done in the past. So, I check and double check all wire connections. What took the longest for me was configuring the Turnigy 9x transmitter.
I'm thinking may be the servo is not getting the signal. The servo is getting power because when I attempt to turn the yaw assembly by hand I hear the servo hum.
I made a video. May be the video will help diagnose what is going on with the yaw servo.
I am stuck in this same situation! Did you ever resolve this? On mine the channel four signal is getting to the APM. But APM is not sending out any yaw signal. I'm going crazy with this.