Just doesnt work, I upgraded to WP 3.6 and The newest

Just doesnt work, I upgraded to WP 3.6 and The newest version of Blog Templates,
I have tried making different default templates, It just doesnt bring accross the menus.
It used to bring over the menus just not into the locations, now it doesnt work at all.
I need this working. What am I doing wrong? The menus checkbox is of course selected....