This may have something to do with the engine specs. These would need to be edited to ensure proper gear ratios at the different notches. If you are talking about AI drivers, you can set slower speed limits at station platforms then set them higher farther down the line. This will keep them reasonably slow, but it will affect other through trains as well.
An alternative might be to use the Max Speed command and set that after the station so they won't go faster than what you set it and eventually after passing a trackmark somewhere, remove that using the cancel Max Speed (I think that's what it's called) to have the driver resume normal speed.
John