This is my private (and uneducated) opinion.
It is a weird thing and cost me three of four reinstallation because
assumed (wrongly) that the system would never come back and I had to
reinstall it.
I do have ultimate on three computers now. What I've decided to do when such
things happen is to wait and never touch it until it comes back and it
always does.
It is my observation that this happens after some updates/upgrades by MS.
Some updates have to cover so much territory you would never believe. Just
an analogy: an installation of SP2 for VS2005 took so long I go absolutely
scared. You feel like the system hung up and got in a loop somewhere.
Thus it may be only first time after an upgrade of anything you perhaps are
not aware about the MS downloaded in your machine while you were asleep. We
haven't seen it in XP for two reasons: smaller OS and the fact that the XP
developer who has since retired and never passed their experience onto the
next generation

were kind enough to give us warnings what the upgrade were
doing.
Your boot will get faster as time goes by. I've seen it. You can also
download a MS baseline Security Analyzer (free from MS website) and have it
run wild. It will show you what other, yes upgrades, you are missing and
should download. This may work either way, of course.
You can also try to make it vLite, I think. There is a list of services you
definitely can do without. It requires a thoughtful approach, you can turn
those off and usually it accelerates things quite a bit. this may give you a
temporary respite until they find a fix to your problem in case it is
universal.
Vista does have a tendency to repair itself but you will have to leave it
overnight at times with the Internet access on.