Sorry to relive this topic but I'm having the same issue,
I was playing it with a ps2 controller and am otg cable on my tablet (galaxy tab E 9,7) and I decided to upgrade it to a red samurai bluetooth controller (actually in my country it's labeled differently but it is yet the same chinese controller)
Though the controller is recognized by the interface of the emulator (and other emulators) and keys are mapped correctly in the profile, and also, the right profile is enabled in each game settings, the actual keying event is not being detected in the games themselves when they are launched. (Tried restarting the game inside the app to see if it was legacy settings or something like that and also closed and open the emulator but with no luck)
My next steps should be deleting the app cache and data and trying starting over and if that does not work, maybe reinstalling. I will try that tonight cause I have to work right now

. But if you guys have any hint to point me in the right direction to fix this I will truly appreciate.