I am having the same exact issue trying to use a Kodak i30 scanner (nicer imaging device for businesses) with their Kodak Capture Lite 6.6 software. It won't initialize the device UNLESS I do a "Run As" and login as the local administrator. THEN it works just fine. You can try this for a temporary fix - it's kind of annoying but totally workable. I'll be doing it until I can figure out which super-dooper Windows 2003 Server permission won't let me run a ISIS or TWAIN device.
Let me know if you come up with something better.
~Gizmo