I have downloaded the latest version of TT but I am experiencing the same symptoms. I used TT to design my theme (along with the main menu) but after porting my theme over to Drupal 7, I cannot identify the block region for main menus. Under structure-> blocks, the main menu is currently showing under "none" region. when I pick a region for the main menu, say MARegion00, it seems to be retaining the main menu that was imported from TT and also the main menu that is assigned to a specific region. Both the menus are also popping up on all admin pages e.g. block admin page, view page etc.. Am i doing something wrong> How can i prevent this behavior? Is there an open ticket already? Thanks!