I tried deleting both menus and then creating the Top menu first and then the Footer, but the same thing happened – as soon as i created the Footer menu, it appeared at the top.
So, I deleted them both again, tried a few other things, and what finally worked was creating a “1_top”, saving it, putting it in the Primary menu location and saving theme locations, and then creating “2_footer”, saving that, putting it in the Footer menu location and then saving theme locations. Don’t know what part of that made it work, but it works.
Thanks for pointing me in the right direction for a workaround. Hopefully you’ve found the bug and it won’t be an issue in future updates.