Can you make sure INI files are used? You can check from the About dialog box on the Help menu.
I customized the three list menus: (each to a submenu)
And I customized the trayicon menu.
When using ini, Recent Files and Macros are missing. Fonts are retained. But all the three are no longer submenus.
Trayicon menu turned to the default.
Recent Folders and Insert list are also missing.
In eeCommon.ini (when just exported and before running EmEditor):
Only these keys are retained in [Macros] section:
In [Recent File List] section, there are only Attr keys (unsorted). No File keys.
Some entries in the Registry are not saved until you exit EmEditor. If Quick Start option is checked, you will need to exit the tray icon too. Please restart EmEditor and try Export again.