I just checked two Vista machines - the scroll wheel works the same as my XP machine. Wheel away is up, wheel towards me is down. No difference. This is on a Logitech VX Nano mouse.
I changed to an old Microsoft wireless mouse - no different.
Here's what I would do in Vista. Uninstall the mouse completely. Then reinstall it. If you can use a different driver, do so.
Also, try a different mouse or brand of mouse.