I hadn't noticed this before even though I use setvelocity quite a bit but you're right.
It does seem to work the first time the command is used but after that it just gives them a nudge.
I have created a ticket for it but a minor bug like this may not get much attention.http://dev-heaven.net/issues/25085
You may be able to work around it though but it depends on what your doing.
If it's for a static vehicle then you could just attach the car to an invisible motorbike and then setvelocity the bike.