All I can suggest

other than a complete new install, is to first scan the Vista system with a couple of anti-malware scanners like the free versions of Malwarebytes Anti-malware and SUPERAntiSpyware.

See if they turn up anything.

Is anything mentioned in the Event Viewer? I wouldn't have thought so on an upgrade, but there might be a clue.

Also, there may be logs about the upgrade that could indicate why the upgrade failed. The Microsoft link below explains a similar, but not identical, situation where upgrading fails;
http://support.microsoft.com/kb/975253

See if you have logs of the upgrade.

Mark