Main menus do not sync with menus invoked from Actions

I'm Using IntelliJ IDEA Ultimate. 

I've made some adjustment to remove some actions on menus in the Preferences | Appearance & Behavior | Menus and Toolbars. I've successfully removed some actions on the main menus, but they were no synched with menus invoked from Actions. for example, In Preferences | Appearance & Behavior | Menus and Toolbars I removed the Action "Comment with Line Comment " and "Comment with Block comment " from the "Code" main menu, but here is the problem: when I invoke "Code" from Actions the results are not synced with "Code" from the main menu.

To summarise: The menus invoked from Actions do not sync with the main menus. 

"Code" main menu:

menus invoked from Actions:

results:

See? They are not synced. I want to sync both of them. How can I do that?