to test your game pad / joystick, you could also use the command line tool
jstest. With that you could make sure that your game pad is fully recognized by the operating system in the first place!
When you are done with that and you can be sure that the OS is recognizing the pads reliably, you can also be sure that it is “only” a matter of how to configure RetroArch and the other emulators (and also Emulation Station via es_input.cfg).
I can also confirm that Duke is flickering at the beginning, but this does not continue within the game. In order to play Doom, you need to add your Doom .WAD files. The one that is initially provided is needed by the emulator, but it is not an actual game.
Hope that his gives you some ideas!?