Game controller not recognized

[LunaMoo]

You should check which change broken it for you ~ here's a list of recent builds(just go in halves between some old build that worked and one that doesn't work to do it in few steps) and then open an issue on PPSSPP issue tracker.

Recently there were some changes to input, to allow detecting dinput devices after ppsspp launches and also I believe to workaround an issue with controllers that had both xinput and dinput at same time, one of those changes could accidently disable all dinput when xinput device is connected at least in your situation.
Likely soon new PPSSPP version will be relased, so if you find which build was first affected, it might be quickly fixed.