The import of UI elements was changed in version 6.0. The unique identifier of each element is its GUID. It may happen that on a site created in one of the previous versions elements exist with the same element names as in version 6.0, but with different GUIDs than they should have in version 6.0. As a result, after importing the site to version 6.0, UI elements are duplicated and not displayed correctly in the UI.
To ensure this will not occur, you need to unify the UI elements on the older site (for example 5.5 R2) before perfoming its export and importing it to version 6.0.
You can do it easily if you apply this script to the 5.5 R2 database.