I have seen this thread Jump links to another page and return back to the first page anchors successfully and I have this problem too.
The menu links work fine if called from the page with the sections on it. However, from another page clicking the menu link takes me to the section above the section I want to go to.
I added /#schedule for instance in the custom menu item. When you hover over the menu the browser shows that it will go to mysite.com/#schedule BUT that is not where it goes.