As of recently, the toolbar configuration behaves very strangely.
One example (I would have many).
EmEditor Version 25.3.0
1) Customise toolbars → Reset all toolbars → ok.
2) Repeat step 1.
3) Customise toolbars
4) Unselect all toolbars except for “Sort”.
5) New Toolbar → Name “MyCustomToolbar”
6) Insert Below → New Text
7) OK
8) Toolbar is shown and listed.

9) Customise toolbars.
→ “MyCustomToolbar” is no longer listed.

Depending on how one does this custom toolbars may or may not appear.
Adding further toolbars can cause previous ones to disappear.