For me the problem was that when I tried to map the left-c button it would (for whatever reason) be the same recognized command as when I tried to map the Right-c button, thus giving me an "already used" kinda thing. I simply got around that by first calibrating the pad in Windows (important to do that first) then when it came to assigning my buttons I simply mapped the Right-c first and left the troublesome Left-c last so it would not conflict.
Hope you can solve your issue as easily as I did.
Here's my Official N64 pad config file if you can't get it going.
Official n64.zip