We had a user that opened up Outlook Web Access and all she could see was her Inbox. She could use the drop-down to change folders, but the Navigation Pane was gone.
I searched the Internet for a solution and several suggested deleting a hidden message in the user's inbox.
Turns out the solution to our problem was much simpler.
The user's desktop shortcut to her OWA pointed to the actual INBOX and not to the OWA main login page.
So, if you have a user that can't find the Navigation Pane, check the shortcut on their desktop first.