I’m new to WordPress and Mantra but, I only have issue in Chrome when using Chrome to manage WordPress. Try clearing your browser cache before testing the site as a user.
Able to successfully remove menu items with plug-in enabled. Existing settings on menu items are restored plug-in is re-enabled after adding a new menu item.
Have a WordPress install that’s just a few days old and have run into the same issue. Tried a few other plugins and finally found If Menu, at least it’s not just me.