I'm on Safari 12.0 and having the same issues.
I have 51 collections in store management and only 48 show in storefront.
I've also tried at least once or twice for the last several day to move my Christmas collections to the front and they initially show when I save it in store management but when I check storefront they aren't up front or even showing as public. When I go back to check management they are in the back again.
I checked to make sure they were set to public.
I noticed this morning that all the Departments aren't showing in the dropdown menu in my "storefront". I signed out of my store and checked to find the same thing.
Here's a screen shot of all that's showing in the Departments menu for my store. I currently have 6937 public products in this store.