It's my understanding that the BIOS reads the state of the JCLK jumper, and uses different BIOS setup tables for each state of the jumper.
My jumper is removed in sig system (DLT3C XP1700+). When running an XP2500+, I tried with and without jumper and noticed no difference at all.
When testing a DUTC XP1700+, it seemed more stable with jumper installed.
Beats me. The only way to know which state is best is to test with and without jumper.
Hope this helps!