You may be hiding it either with the keyboard shortcut or the menu option.
The keyboard shortcut to show/hide the bookmark bar is: command+Shift+B
Other than that you would have to be clicking View->Show Bookmarks Bar, or View->Hide Bookmarks Bar, which you would be aware of though.
Restarting Safari should have no effect on the visibility of bookmarks.
If you are sure you are not doing either of these, we have to do more research into the issue...
Hopefully I understood you correctly, or are you actually losing all your saved bookmarks items each time where you have to re-add them?