I answered a similar problem in this thread:
http://www.eng-tips.com/viewthread.cfm?qid=177301&page=1
in regards to getting the license working properly.
However, even with having Pro/E working, it runs painfully slow in Vista.
makidproe,
I've had many random issues getting things to work in Vista which generally all amount to it's new way of handling permissions. Go into your program files folder on whatever drive you installed it (probably C:\Program Files\)
then go into the "flexnet" folder and then the "bin"...
