I have my main bookmarks in alphabetical order and those in the bookmarks toolbar in my preferred order. This is the same on 4 different PC's, all of which are synced in FF.
However, whenever FF opens after the PC has restarted it re-organises the bookmarks, both the main list and those in the toolbar. It always re-sorts them into the same order (but not alphabetical) and it moves all the separators on the toolbar to the end. This happens the same every time and on all PC's and has happened since v16 (I'm now on v18 and it still does it).
I've tried removing the 'localstore.rdf' file from the profile folder but that hasn't made any difference.