From the On Target website:

The bow performance slider can be used to change bow efficiency as it relates to the IBO/AMO velocity. Changing the slider will alter the the program calculation for arrow velocity. This allows the user to quickly synch the program to a calculated or chronographed arrow velocity. Altering the performance factor will also affect the way the program makes shaft selections on the Spine Match Tab. Using a higher performance factor will result in the program selecting stiffer shafts. A lower performance factor will result in weaker shafts being selected.

After reading this, it sound like the software engineers intended the performance slider to be used to synch the predicted velocity to the chrono'd velocity. And they also sound like they knew what they were doing by in turn allowing this to affect the spine match tab. This just makes intuitive sense to me that a higher arrow speed would require a stiffer shaft. That's consistent with what I know about archery and basic physics.

If your predicted vs actual speeds were off by more than say 15 fps, and the arrow spine didn't change at all by synching the program to your chrono, I would think something is wrong.