The sad truth is, after all these years, n64 emulation still sucks.
At least 65% of the games aren't emulated properly, and even if they are you have to jump through several hoops like special cfg files, special settings and even multiple emulators, depending upon which game you wish to play.
I love the n64 and it's games, but imho it's just not worth it to run the n64 on your pc. Perhaps someday, when the developers get a clue, combine all of the emulators into one and make the emulator "automagically" jump through all the hoops for you will it be a viable idea.