Are you having this joystick issue in all of the new builds (since I made the mainline PR) and not having this issue in the Google Play build on the same device? If so, to me that sounds like an SDL Android input bug, since none of the joystick input code has changed since the Google Play version, but I did update SDL from 2.0.5 to 2.0.8 as part of the mainline PR in the hopes it would resolve our software renderer issues, but it doesn’t seem to have fixed them and may have also introduced this bug on certain devices only (like yours). We could look at downgrading back to SDL2.0.5 and sticking with that instead. I’ll also make a note to sift though SDL bug reports and see if anyone else has patched it or experienced the same issue.
Could I also ask what Android device and version you’re using?