Had the same problem with my Cintiq 12WX not working after restarting. It didn't start doing this until about a month after installing Windows 7. I'm not sure what the trigger was but I think it may have had something to do with me playing around with the tablet features in Windows 7 to see if I liked it or not, so I suspected that's what was interfering.
Anyway, this fix worked for me:
Reinstall the Wacom
driver again so the tablet works (no need to uninstall the
driver, in fact I'm not even sure if this step is necessary). Load msconfig, go to the Services tab, find the "Tablet PC Input Service" (sorting the services alphabetically will help you find it easier), and then hit the checkbox to disable it. Restart. Tablet should work.
Of course if you actually use the tablet PC features then this won't be the fix for you, but it's straightforward, got rid of the offending service, and also removed some features that got in the way.