I just moved a blog to multisite and now the custom menus are broken. They were working fine for single site. I've tried it with both the Responsive and Eslpanade themes thinking it was a theme problem, but deactivating polylang makes it work.
Here is an old thread that seems to have had a similar problem:
Also, what is weird that when I select the "Primary Menu English" checkbox for a menu (or whatever that option is called for other themes), or if I go through Customize Theme and select teh menu there, the menu is reset to blank immediately (or the checkbox cleared).
Please let me know if you need any more information.