60FPS is displayed by Project 64, I really think it is misnamed as it is really the number of VI's being performed, the framerate is half what it says, 60 VI's = 30fps, 50 VI's = 25fps.
By the way to back this up, I know for a fact the N64 NTSC does not go above 30frames per second and the Pal one doesn't go above 25. So this theory is based on logic. PJ64's FPS is equal to 1964's VIs;
Adjust the counter factor to a higher number, if its CF1 set it to CF2 and so on till it feels more accurate.