I found the solution. Somehow, when I installed Woocommerce, my main menu was no longer selected under “Menu Locations” under the menu tab. So it was showing a default menu. Once I checked the box “Enfold Main Menu (Current: Main Menu)” it started working.
robinkholland, would you share your solution? I have the exact problem except I am using the enfold template. I have a main menu and it was fine until I installed and activated Woocommerce and it added several pages to my menu and now the menu is not in the order I have set up. The only way to get the other pages not to show under the menu is to make them drafts.
