are both connected via usb or is one using a ps/2 to usb adapter? if the usb bus is busy there could be delays. if you use an adapter then the polling rate means jack as it doesnt need to poll and is forced interrupt instead.
depending on how the website records responses internet lag could be a factor unless you both use the same internet and you are sure this is not an issue.
general computer slowdown due to age of the os install, age of the components, malware, etcetera could also bog down the test.
i doubt it... but windows mice settings might be a factor.
in general... it could be a multitude of things. besides just wanting to get the best time does this really affect you at all?