so you're on Vista fully updated, ie SP2 right ? OK and this happens only when you install the IS. My best guess is that the firewall might block some traffic necessary for Windows validation, as this is checked each time you reboot. May be no internet traffic but some Windows internal traffic... I've had a huge issue, by my fault, recently when deleting manually the content of the firewall rules file. When rebooting I found an empty desktop, went into safe mode and found in Windows events that tens of errors related to DCom stuff and NT/authority happened. Anyway I suspect the firewall of messing with the rules in a general way, and this could be the source of your issue. I'm not sure at all, just guessing...
Another possibility is the behavior shield, try to deactivate it...