You might be able to clear faults and adaptations to see what happens. You'll need a scan tool that can see the transmission code to reset it. I have seen this issue with a bad module, paddles and/or the shifter itself. Also, in a few cases a bad battery. Did you plug into your OBDII and look to see if there are any faults present in the system?
I'd also suggest you post this information in this article here:
MINI Cooper Automatic Transmission Fluid Change (R50/R52/R53/R56/R57 2001-2015) | Pelican Parts DIY Maintenance Article. Nick might also have some valuable input for you.