I had the same issue with the same controller. I suspected it was the Xpad driver and was correct after updating everything else individually.
I'm not certain it will fix the issue, but here is my working Xpad driver's entire folder.
Working Driver: https://drive.google.com/file/d/1HYT5lnioWIvuF3LuNHe4Wf91DzfLM5-k/view?usp=sharing
These go in /opt/retropie/supplementary/xpad, but everything in there requires Root access to alter.
SSH Method: https://retropie.org.uk/docs/FAQ/#why-cant-i-ssh-as-root-anymore
I hope I was helpful.