I had a similar problem.
Tried all the recommended troubleshooting procedures:
– Disable plugins
– Change template
– Create a new menu
– Modify .htaccess file
Even used databases backups.
All of them above didn´t fix the issue.
Then I found the Manage Locations tab at Appearance, Menus. It´s the right tab next to the “Edit Menus”. There is the option to select the menu; and, everything then worked fine.
Hope this helps.
Thanks Pablo. As long as I have a menu in there, everything is fine. If I leave it blank (as it was) the categories get copied into the menu. I left “Home” in the top one and shifted my actual menu to the second one and all is well. I’ll consider that a resolution for my purposes and move on to the next headache. 😉