Please note that official support for this menu version has now ceased. There are still plenty of users, though, and the forum is still running. Some of our long-time users may be able to help you out.
If I understand corrctly, your submenus in a body frame are not lining up with the calling mainmenu items in a header frame. There are two parameters that you can adjust in the menu_array.js files to reposition submenus in a frame:
Frames_Top_Offset=0 // adjust from top of submenu's frame
Frames_Left_Offset=100 // adjust from left of submenu's frame
If they are not already there (and set to 0), these two parameter should be added to the list at the top of the menu_arra.js file, along with timegap, followspeed, etc. It may seem backwards, but you should adjust these values in the menu_array.js file that defines your main menu, not the .js file that defines your submenus.