This can be caused by a corrupted places.sqlite or by importing a HTML backup that created those extra, normal, folders instead of placing the bookmarks in the existing root bookmark folders that have the special icons.

You may have to cleanup this manually and remove the bookmark folders with default icons and move the bookmarks out of those folders.

You can check for problems with the places.sqlite database file in the Firefox Profile Folder.

• 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

Thanks for the reply, but I ran all the checks with the maintenance addon and I also checked for corrupted sqlite files. That's not the case.

I tried to manually delete the folders but I can't (option is grayed out).