The proper way to bench (if you want the highest possible score) is to turn off V-sync and set your refresh rate to 60hz.
My guess is that 3DMark2K1 may automatically take control of your refresh rate for the bench, then it'll forget to return it to the previous setting afterwards. If your Display Adapter refresh rate is set to "Adapter Default" or "Optimal", try setting it to a numerical value (anything over 70hz should be fine for your eyes).
Hopefully, when you close 3DMark2K1 the OS will take back control of the refresh rate and set it to where you want it.