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I've seen this behavior too... I'll describe the problem:
1st: the differential brakes axis assignment gone missing (NONE) and yaw axis kept assigned and working right (no brake applied with yaw movement)
2nd: When I re-assign brakes axis, yaw start to input differential brake as well and the actual brake pedals don't respond at all.
3rd: When I close the sim and open the same plane, differential brake axis assignment is missing again.
4th: If assign diff. brakes now works right.
Try this steps and you may overcome this bug until is fixed... (did you fill the bug report?, I didn't and I think I should)
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