yeah if the gc controller is connected on port 1 he takes controller 1 port whle there and most games do not let you use port 2 or 3 or whatever to controll them.
also if you are using latest nintendont 4.439 all gc games should work perfectly, the problem is sometimes people have bad dumps or settings enabled that some games dont like wich could be your issue since i have no idea what settings,version or sisos you are using, but all the gc games work perfectly.
I got these roms from emuparadise to test. Never had bad dumps from that site?! And I think I have the latest Nintendont version - also I was setting up my Wii completly up to date a few weeks ago...