could someone try to see whether that is a general issue....
AP3825e running 10.31 (ROW)
If you cset the AP and the AP connects again to the controller the antenna selection is gone and I need to set the right antennas (and also set the radios to admin mode on) again.
In my opinion that shouldn't happen as the controller shouldn't loose that setting.
I've only tried it with a AP3825e but it could be that it's the same with other AP models with external antennas.