Another interesting thing, I have an Arduino Duemillinove with an Xbee shield attached with an Xbee 900 Pro Duck Antenna that I use as the receiver for my ground station. Normally the light on the shield is lit when any Xbee is plugged in, however when i plug in the problematic Xbee, there is no light. This leads me to assume that it is permanently shot, I don't see what could have caused the failure during normal use.
I'm sharing this to see if anyone has experienced similar issues, and if they found a solution. If not I'll just buy a new one.
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We're looking for a way to modify the code to prevent this, but for now always disconnect the Rx before powering on your plane.