Not quite sure what you mean. The navigator view will list all of your projects as a folder tree, each project being the at the root level. Is this what you mean? Or are your other projects physically being copied on your hard drive to the new project folder?
They are physically being copied.
I create a new project folder that is empty and the folders appear. I delete them and they reappear.
I am using cfbuilder as a plug in on top of a flashbuilder 4 eclipse install.
What are the folders being copied to your blank project? By default you'll get a ".settings" folder a ".projects" file and a settings.xml file.
They're probably the project files. Stuff like .settings, .project @ settings.xml? if it's that lot, that is your project.