New Blog Templates plugin copies menu, but not the setting to associate it to primary menu

I just updated to latest version of the New Blog Templates plugin and when I go to create a new site it copies everything over, including the menu, however it doesn't copy over the main menu I have setup as the primary. This is more important for the clients that are creating sites on my network. They most likely will not know to go to the menu admin page to choose select the main menu in the drop down and save to activate the menu. The weird part is that it selects the main menu as the footer, but just not activating the main menu as the primary. Any thoughts?