Do you use any of these extensions which affect bookmarking in Firefox 40:

• IE Tab, IE Tab 2, IE Tab Plus, etc.: you'll need to disable
• Tree Style Tab: you'll need to disable
• Tab Mix Plus: you'll need to update to version 0.4.1.9

Actually, reading your post more closely, did you cross-restore between different Windows users? Note that Windows uses a unique SID for each user account, and that same-named users are not the same user as far as Windows is concerned. In that case, you might research on a Windows forum how to globally change the permissions/ownership of Firefox folders to the current Windows user.

What your second message said got me thinking. So I deleted the profile folder, which I copied, and opened firefox, so it would be as though it had just been downloaded. Then I went into my flash drive, which had the copied firefox files in it. I went into the import function in bookmarks and went to the restore, and choose the latest backup of bookmarks from the flash drive. Now I just have to re-enter all of my passwords. Thanks for the response, it got me thinking, which led me to fixing my problem. And in case anyone else uses this, I have no addons downloaded.

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/

• 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