Are you confusing "history" with "bookmarks"?
Ctrl-b = bookmarks
Ctrl-h = history
History DOES disappear when you clear Private data, bookmarks don't.
Also, you can "organise" bookmarks to appear in the Bookmarks Toolbar, or not (default is not, to avoid clutter).
But it sounds like the toolbar is not your problem.
added:
There is no "navigation pane", but there is a navigation toolbar.
There is also
Firefox online help & support
SD