Hi Michael, I had a similar issue and had originally posted over here
I further explain what I believe Deamon77 is describing in the last paragraph below...
Great plugin!! Thank you very much for developing and sharing! This plugin is very close to what I am looking for however I noticed a few things while testing -
In my original blog I had created custom post types - the post types had transitioned over but any of the posts I had made within those post types had not -
Also in the settings > Reading > I had set up a static front page as well as designated which page is to be used for the blog posts - for some reason in the new cloned blog from the template these settings were ignored when the new blog was set up.
When setting up a new site / blog I have noticed that the radio button is visible in all new blog / new site registrations but it only actually works if you are logged in. Also I noticed that if you are logged in as "super admin" it works but if you are logged in as a user that was created and try to activate an additional site under your user name then the custom menu created in the original blog template (appearance > menu) gets created and is listed in the drop down menu and its active but the menu somehow got erased and is basically an empty shell and leaves no menu visible on the new cloned blog.
Do you see these as possible bugs you would be able to fix?
Again thank you very much!