Are you using Sync to sync the bookmarks?

You can check for problems with the places.sqlite database file (bookmarks, history) in the Firefox profile folder.

• Places Maintenance: https://addons.mozilla.org/firefox/addon/places-maintenance/

See also:

• http://kb.mozillazine.org/Bookmarks_history_and_toolbar_buttons_not_working_-_Firefox
• https://support.mozilla.org/kb/Bookmarks+not+saved#w_fix-the-bookmarks-file

If the Places Maintenance extension can't repair the places.sqlite database file then remove all places.sqlite file(s) in the Firefox profile folder to make Firefox rebuild the places.sqlite database file from the most recent JSON backup in the bookmarkbackups folder.

If you use Sync then best is to disconnect Sync (temporarily) while performing maintenance/repair efforts to the places.sqlite database.

Use with Extreme Caution;

Bookmark Duplicate Cleaner {web link} Scans for bookmark duplicates and allows you to delete them

Bookmarks Checker - check for bad links {web link} Check favorites for broken or bad links. It checks for bad links and displays a report if it finds something. Check for 404 links, timeout links.