By “WordPress Custom Menu” I said I meant that you create your menu manually in Appearance > menus, by opposition with letting WordPress create the menu automatically from whatever pages you create.
“There are the same number of menu items on both versions of the site. Since the other site works fine, I don’t think it is a WordPress problem.”
menu are only managed by WordPress, so either something is wrong with WordPress, or some combination of things (plugin / theme is causing the issue).
One of the known issue with WordPress menus is the Max variable parameter I mentioned. these variables are used by the menus but also by plugins and theme. As a result, a specific combination can lead to the max being reach and causing all sort of problems (Xtreme uses a Lot of these variable and can definitely contribute to reaching the default limit.
This is why a good thing to do regardless, is to set this max variable to 20000 using the appropriate method as explained in the article I referenced.
Other things you can try are:
Deactivate ALL non weaver plugins and see if that makes a difference (if it does reactivate one by one)
Redo the latest WordPress Update from the Dashboard > Update