I'm not quite sure if parallax is correct word.
You have homepage main menu which uses anchors to determine where page should scroll to, when menu item is clicked.
Anchors refer to ID of element holding each part. While moving modules between locations, or rearranging them, they ID's change because they are defined dynamically.
It would be easiest to use firebug or chrome developer tools to find correct id and change it in menu editor.
If You have trouble with that, please share sites url, and point which menu items scrolls to wrong place - then Ill be able to show You what needs to be changed.