I am having a similar issue as described here -> https://premium.wpmudev.org/forums/topic/i-keep-tring-to-shave-the-menu-structure-and-sub-items
As I try to add items, they are not saving. I have tried flushing browser and wp cache as well as multiple browsers. Here the steps to replicate:
1. Go to the settings for the main nav
2. Try to add Polos under Kids -> Casual Wear (same place as Jackets)
The item will save, but not in the right spot. Any ideas or thoughts would be helpful. Thanks!