How to do a clean install with Windows Vista upgrade disc 
1. Power up the machine and put the Vista DVD in right away.
2. Vista install will begin and ask for a key,
DO NOT TYPE YOUR KEY, just click next.
3. You will get a list of choices of the different editions, choose the one that you have.
4. When Windows Vista finishes installing and you get to the Desktop,
put your Vista DVD in and do the whole setup agian. You have two options,
upgrade or Custom. I recommend choosing custom and begin agian.
This time when you are asked to type the key you do and it will be accepted
and you will be able to activate.
So basically you are installing Vista twice in a row on top of it self.
By choosing custom it will wipe out the
old install and give you a true clean install.