jQuery
Prototype
I can discern no consistent difference in timing or performance. Occasionally, however, jQuery will get ahead of Prototype, only to have Prototype catch up some time later.
When they "hang" or "glitch", they appear to do it together, implying that the entire JavaScript engine is hanging. So the problem can't be isolated into one library or the other in a single page.
The problem seems to appear only in Firefox, and typically shows itself during the first seconds after the page loads.