Can you be more specific.
Are you creating your menus using WordPress Custom Menus in Appearance > menus.
When you say menu items get duplicated, do you actually see them duplicated in the list of menu items that appears in Appearance > menus.
If you have a lot of menu items, you may be hitting a variable limit in WordPress.
The article below may help you increase the max variable that can cause your menus to go crazy or disapear