It could be the version of 1964 that Console Classix uses then (1.0, when 1.1 is current), or maybe the plugins they're using. I'm not sure how that whole plugins business works.
I installed Project64 1.6 (not Project 64k), and I've tested it with Super Mario 64. As far as I can tell, it seems to run at full speed. I have an N64 controller (knockoff, not original) with a USB adapter, which I think is a must for N64 games.