Help, My FCE Ultra GX Emulator Can't Multi Player

Hi newbie here. I have just installed the latest version for the FCE Ultra GX Emulator. My roms are loading fine, but trouble is when I try to playing multi player for some NES games like Teenage Mutant Ninja Turtles 2, my 2nd gamecube controller is not responding at the Start Menu. I can only use Controller 1 to play. I changed Controller to Nes Controllers (2) but to no avail. :(

If you have a wiimote and a gamecube controller, you need the gamecube controller plugged in port 2

Thanks for your reply, I am using 2 gamecube controllers and tried connecting them on all the ports, only 1 is working.