Robert, I think I found the issue. The menu cannot have more than 90 pages or it blows out the menu and defaults to the alphabetically list (view all).
There are work arounds and plugins for custom menu but the thread that I saw was 3 years old. See link below:
https://www.ads-software.com/support/topic/menu-size-limit?replies=33
I figured out that I can condense some of my sub-navigation into html links on the main header pages and the navigation menu fits like it did pre-4.0. This is my work around that I just discovered tonight. Keep me posted on the templates that you are going to try.
Thanks and Good luck.