In a car, tyre pressure can affect the speed reading - as can swapping the wheel for one that is a different size, with a low-profile tyre etc.
On a train, I presume there's little to alter the reading if it's done on a metal wheel revolution? I guess if it slips that would mess things up, but only for a fraction of a second.
Do modern trains also use GPS to measure speed (even as a secondary option)?