Yesterday (9-Sep-2016) my bookmarks in FFP suddenly disappeared. In addition, when I click the bookmarks icon, the panel of bookmarks no longer appears on the right side of the screen. If I select Show All Bookmarks, a "Library" window opens, but is empty. If, from that Library window, I take the option to Restore (under Import and Backup) , I get a pop-up saying "Unable to process the backup file". I tried numerous back-ups that Firefox had created, but got the same message every time.
Finally, I saved the entire FirefoxPortable directory to my C: drive, uninstalled FireFox Portable, and reinstalled it (from a new download from PortableApps.com). The installed version is 48.0.2. This did not fix anything. The Bookmark icon still doesn't display the right-hand panel of bookmarks, and if I Show All Bookmarks and try to restore one of the backups from the saved FireFoxPortable directory, I get the same error, "Unable to process the backup file".
Additionally, Ctrl-D fails to open the save bookmark dialogue. Right-clicking a link and choosing Bookmark This Link also fails to save the link.
Additionally, (unrelated perhaps), changes I make to the History setting under Options>Privacy fail to persist.
