Sync isn't moving preferences or bookmarks correctly, and is deleting bookmarks off my machine

So, I got a new box, loaded Firefox on it and decided to move everything over with sync. I set it up on my old box and everything uploaded fine. On my new box, however, it downloaded my add-ons, my history, and just about everything except my preferences. That would be fine, however it also only loaded a few of my bookmarks, seemingly randomized their order, and even deleted a few. To make matters worse, it synced that data to my first box. Luckily, I have a backup on my first box containing the bookmarks, but I can't get it to load. What should I do?

Try to disconnect from Sync, quit Firefox, delete places.sqlite, restart Firefox, and re-set up Sync.
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

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