Considering that it's not even a BMW tranny...
I believe that model transmission IS adaptive, so you could try disconnecting the battery and letting it sit for 30 min to an hour to clear everything and start driving easy on it for the first little while until everything feels "right." If everything is cleared, cool - it was just a computer issue - if not then it could be time for a fluid change (which I doubt because you said since the rebuild...) or they could have done something wrong during the rebuild.
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