I think Kenny beat me to that :-) Also, the original exec.library didn't have any proper accouting so I guess most applications measured CPU with their own code. Probably the code that measures the use just doesn't work under the JIT.
One other possibility is that the CPU really is at 100% - grabbing the framebuffer to a file could easily swallow up all the CPU for a short time...
Moving on, I have to say its all shaping up a treat :-D