Joel Spolsky has an article that touches on one of the big risks of Rapid Prototyping. The risk is that if you focus on getting a polished UI first, particularly if you implement it (even in a prototyping tool), non-technical managers will get a mistaken notion of how far along you really are, and you'll get beaten up for slacking, or have your schedule slashed. I've seen this happen. It isn't pretty.

If you're going to do Rapid Prototyping with your customer, do it on paper.