When using Calypsoify on WordPress.com, I see all of the core menus, even when I select the "Plugins" menu in Calypso for the connected Jetpack (or Atomic) site.

This is what I see:

This is what I should see (notice how only the plugins menus remain and all core menus are gone from the sidebar):

It looks as though the code to remove core menus is no longer working.