I am having a similar problem but I believe it is because I simply do not know how to use this product.
I don't know much about php or includes but I will run the steps I have taken through with you to help identify where I have gone wrong.
1. I have created my index.html page (well really it is a purchased template). I have identified areas which need to be plugins i.e image slider, tabbed panel (for news content) and navigation.
I have also identified the include areas i.e. header, footer, background sidebar.
3. So back to my index.html i still have the areas I want to use as includes on the page. I convert my page to DWT.
4. This is where I am stumped. Do I need to define editable regions or do I run the framework builder theme wizard straight away? If so how does framework builder no which areas i want as includes and how to divide the page?
When I defined editable regions for main content and sidebar and ran the wizard I came up with a blank page.
I really just need some direction in understanding this. Please if anybody knows how to use this extension any help would be much appreciated.