I never, ever, never, ever, NEVER do "upgrades" on OSes. I believe the fresh install is always the best way to go IMHO.

My VISTA-64 install went without a hitch. I actually purchased the Ultimate Upgrade Edition, but the Einstein at Best Buy actually gave me the non-upgrade version when I picked it up.

Sorry I don't have any suggestions - but I do think a clean install is the way to go. I love VISTA-64, it's been rock solid for me.