I'm having an issue where the APM is causing the aileron controls to also move the rudder.  The problem does not happen in the first 30 seconds of so after powering the board, but after about 30 seconds, something flickers around with the electronics and then all of a sudden when I move the control for the aileron the rudder will move too.

I made a video.

Any suggestions?

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Are you sure you haven't set it to elevon mode? If not, reload the code, and do a RC setup again. 

I've never seen that before. 

You need to check what mode you are in. The APM takes 30 seconds to boot. You have manual control until the boot sequence is over, then it will switch into the mode you have set. In stabilize and other fly by wire modes when you apply ailerons it mixes some rudder as well to keep a perfect turn.

See http://code.google.com/p/ardupilot-mega/wiki/FlightModes
See http://code.google.com/p/ardupilot-mega/wiki/StartingArduPilotMega
And how to select the modes http://code.google.com/p/ardupilot-mega/wiki/RCSetup

Also see http://code.google.com/p/ardupilot-mega/wiki/Sixmodes how to switch into six different modes from your transmitter

Hope that helps

Set the rudder mix parameter to zero.  If the behavior you are seeing goes away with that set to zero then the behavior you are seeing is normal.

Awesome.  This worked.  Thanks.

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