I started developing the application I use for controlling my network on my old XP Pro box, but moved over to Vista 64 in February and everything built and ran without any issues. I didn't do much with the samples when I started the project other than look at the code in a couple of cases to see how things were done.
You know, there was one Windows Update that I applied that has to do with USB that you might try applying - search for an optional update titled "HID Non-User Input Data Filter". I applied that update to fix a screensaver issue, but I can't remember if I had even tried the ThinkStick and SDK on this system before I applied it.