Same here. Firefox seems to think it knows where I want my bookmarks to go better than I do. There's no rhyme or reason either as to where they move or why. Personally, I'm just trying to organize really old bookmarks that I've collected for too long. After that, I'm moving them over to Chrome and saying fuck it to this mess.

Do either of you use Sync? There is a possibility of data rearrangement in the Sync process. Otherwise, it sounds suspiciously like your Places database -- the file that stores bookmarks and history -- could be corrupted.

The Troubleshooting Information page has a "Verify Integrity" button to do a little light maintenance on the Places database (where bookmarks and history are stored). You can open that using either

• "3-bar" menu button > "?" Help > Troubleshooting Information
• (menu bar) Help > Troubleshooting Information
• type or paste about:support in the address bar and press Enter

Then scroll way down or use Find to search for Integrity in the Places Database section. At first, nothing will seem to happen, but then several seconds after clicking the button Firefox should report some diagnostic results below it.

If the report looks positive to you, you can exit/restart Firefox to see whether it helped. If the report indicates trouble, you could copy/paste it into a reply for comment.

If you use Sync then best is to disconnect Sync temporarily during troubleshooting.

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

• use "Verify Integrity" on the "Help -> Troubleshooting Information" (about:support) page
  in case errors are reported close and restart Firefox and retry

See also:

• http://kb.mozillazine.org/Locked_or_damaged_places.sqlite
• https://support.mozilla.org/en-US/kb/Bookmarks+not+saved#w_fix-the-bookmarks-file

If "Verify Integrity" on the "Help -> Troubleshooting Information" (about:support) page cannot repair places.sqlite then remove all places.sqlite files in the Firefox profile folder. Firefox will rebuild places.sqlite and restore the bookmarks from a recent JSON backup in the bookmarkbackups folder.

• keep a backup copy of places.sqlite in case a new places.sqlite database has to be created
• http://kb.mozillazine.org/Unable_to_process_the_backup_file_-_Firefox

You can use the button on the "Help -> Troubleshooting Information" (about:support) page to go to the current Firefox profile folder or use the about:profiles page.

• Help -> Troubleshooting Information -> Profile Directory:
  Windows: Show Folder; Linux: Open Directory; Mac: Show in Finder
• http://kb.mozillazine.org/Profile_folder_-_Firefox