Hi Ketih,
It sounds like the Form Settings on the users Main Menu are inconsistent, just like Frank Wang has said.
An example below, you can see I have unchecked the Item Master Data from the Main Menu Form Settings, but I can still access via the Top Menu.
Click on the Main Menu, then choose the Form Settings icon (Circled below in red color) and see if the missing menu items are unchecked.
Kind Regards,
Nick Lakasas