Hi,
I hope you turned ON the ‘Admin menu access restrictions’ at popup opened after you click the ‘Update Network’ button under ‘Network admin->Users-User Role Editor’.
What is not synchronized?
You have to have the same admin menu at all subsites, that is the same list of active plugins, the same active theme. If admin menu differs from subsite to subsite, it will differs under the URE->Admin menu too.
Give me more details on a problem with hiding menu item. What plugin created it? Show a screenshot of ‘Admin menu’ window.