This caught me out big time. And I thought it might be of help to someone else to post my experience even if it was foolish.
The scenario: I have two AP one with V1 shield, Thermopile sensors. Second one with V2 shield with IMU +V2 I only have one GPS EM406 that I swop around (waiting to get UBlox) for second AP.
The problem: I could not get the throttle to work on the First AP every ting else work fine, after rereading the manual rescan the discussions and blogs for similar problems I found some and try all the options only to end with the same problem –no throttle-. Now I started to swab shields around. I want to add that if I remove the shield the throttle works fine.
The result was and a good lesson not to take short cuts when building. When I soldered the pins of AP1 I have also soldered in Pin 13 so instead of de-soldering pin 13 I have just cut the pin flush to the plastic base. Everything was fine till I used Velcro to strap the AP to the base in the airframe it put enough force on the shield to make pin 13!! . I will not repeat the names I called myself.
The lesson Read the manual on the lines and between the lines and do not take any short cuts it will bite you!!