I am sorry, I wrote you solution before but it's not posted because something disturb me and I forgot press Add answer button. It's happens when you do more things at once.
Ok, just update to latest github, reason was in e107 itself, it's now fixed (some legacy issue).
If you don't use copy already, I would recommended you to do it. Just copy all folder, rename it and change theme name in theme.xml file. When I find time, I will do update for 2.1.5 with new things and it could be change your site (expecially sitelinks in footer and sidebars - I really dislike how it's done now)
Thanks for list, I will test it with these menus too. Don't you want to share your site url?