When you say “same main menu”, the important bit is that FancyMenu tracks layouts per screen identifier and only applies them once customizations are enabled for that screen. Going to Options disables the current screen (tod main menu) and you might not have saved/enabled the Title screen layout for that identifier yet, so it doesn’t reload when you return via Options. Jumping back from Multiplayer counts as “leaving a screen that already had customizations enabled”, so the layout still shows.
To fix it, open the Title screen, press Ctrl+Alt+C → Customization, and make sure “Current Screen Customization” is set to Enabled for the Title screen, then create/save a layout “for the current screen” (see the Getting Started guide). Once that’s done, the layout will load every time the Title screen opens, regardless of whether you came from Options, Multiplayer, or any other screen.
If you want the same content everywhere without worrying about screen-specific toggles, consider using a universal layout instead (see the Universal Layouts page).