problems with pitch....ardupilot 2.5

My rover is setup usual config...1.3 throttle steer....my issue is pitch..im trying to make pitch input 2 ardu...and output 2..make it control a servo...it does work up until the ardupilot is booted up and no more led flashing...so its something to do with the ardupilot..i know i cd re route the cable to bypass that ...but i want everytjing on the ardupilot board.ive tried changing the pitch channel to 6...or 7..but no change.it works onchannel 2 but once ardupilot has booted up it stops working...

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