You mean the Anbernic RG-350M? Might have to do with 640x480 output, i'm not sure if SDL on it does software or hardware scaling (the game requests 320x240 mode).
I haven't implemented joystick/gamepad support in the SDL versions - i might do that at some point. Though the engine itself doesn't really "know" about gamepad (originally the game was written for DOS with keyboard-only input), the versions that have support for gamepad simply generate fake key events, so it wouldn't be that different from using the D-PAD. But i might try it anyway in a later version.