When I add a menu item, Joomla shows all menu items on all menus as if they are sub-sub-menu items, ie with a |—|— before the name in the menu manager.
This breaks the menus, or adds "root" to the URL (ie http://www.example.com/root/pagename), until I click rebuild, which fixes it.
This seems to have been happening since I updated to 3.5.0, though I have found previous examples of people complaining about "root" appearing in their URLs who have just been told to click rebuild.
I have also tried it on a second 3.5.0 site, and the problem does not happen there.
I suspect a rogue database entry somewhere. Any ideas?