If you try a new profile and enable ubufox are you able to reproduce this?
Once you disable ubufox did all your bookmarks show up that you were expecting?
Did you restart firefox after upgrade?
** Changed in: ubufox (Ubuntu)
Sourcepackagename: firefox => ubufox
Status: New => Incomplete
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FF Bookmarks toolbar contents don't display if Ubuntu FF Modifications 0.6 is
enabled, in Intrepid
https://bugs.launchpad.net/bugs/329871
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