The wizards are just a guide on how to setup a project. If you're having an issue using the wizards due to your configuration then you should take the time to familiarize yourself with what the wizard is doing for you so that you can manually setup a blank project yourself with the proper configuration.
Alternatively, you can disable this "shared folder" feature whenever you need to create a new project with one of these wizards. I would imagine that this would not cause any further issues for your project after is has been created.
This also sounds like a bug in either Visual Studio or VMWare Fusion than DarkGDK.