that's strange... I only have on gc controller right now, a wavebird, don't think I've tested it in the 2nd port... well maybe I should before getting another one then!
yeah it took me awhile to figure out, I have went through and tested every feature of all the emulators on that disc and for the longest time i was convinced the 2 player feature didn't work till i went and grabbed a standard instead of the 2 wavebirds I had already plugged in and it worked just fine.
Ps - there is No N64 emu on the cube or wii