Calibre now has 2 different sets of preferences
The Main (GUI) Library Preference
e-Book Editor Preferences
Preferences:Behavior: Toolbars (a tab) is used to add-remove toolbar icons in the main GUI.

Remeber that there may be 2 modes for some items Connected (and Not Connected) They need to be set independently (when the proper condition has been met)
The e-book Editor also has 2 (subtle) modes (Edit: Preferences: Toolbars (Side Tab)
Global (on the main toolbar), applies to the Book
Current Tab (on the Tabbed Window) Applies to that edit TAB (file)