I have a similar problem with CFB-full beta 3. When trying to create a new project this morning, it seems to insist that the project folder already exists when it does not.
Could you check in the physical location if the .project file exists?
Also are you using a fresh workspace?
I'm running into the issue right now.
What I'm doing is a checkout using svn/subclipse and trying to create a new CF Project.
Instead of using the default, I'm trying to use c:/inetpub. I know thhis project has never existed on this laptop before nor one with the same name. I just added the code to the repository & it's a freshly wiped windows 7 laptop. CFBuilder shouldn't be telling me it already exists.
Now if I do it a different way and go to projects and create a new one via checkout projects from SVN AND I don't try creating a new CF project but into workspace name "djcgc", it works.