Attempting to compare percentiles on the COMLEX and USMLE is really meaningless. The fact is, the level of competition is much greater on the USMLE. This is probably related to the fact that allopathic schools have much higher entrance requirments, MCAT scores, etc.
Some purely anecdotal evidence: Most people at my school who scored 99% on the COMLEX and then took the USMLE got scores between 235 and 240. These are strong numbers, but nowhere near 99%.