I was experiencing the same problem.  Ubuntu 8.10 on an XO (OLPC)
laptop.  I had reported it here:

http://ubuntuforums.org/showthread.php?p=7040160#post7040160

And another user echoed the same problem as well on a DellE520, ff3.0.8,
jaunty.

I tried gregory's suggestion.  The short answer is that it was bookmarkbackups 
that was the problem.  This was a pretty much new install/config (I noticed 
nearly right away that bookmarks weren't working
 -- I had never been able to successfully save a single one after a restart), 
so I still think there is some kind of bug in terms of why did this happen, 
although it's nice to have a fairly simple workaround.

More details about my exact steps taken are below.

- Rich

Disabled Flashblock 1.5.9.
Restarted firefox.
Added bookmark.
In menu.
Restarted firefox.
Bookmark gone.
Disabled Adblock Plus 1.0.1.
Restarted firefox.
Added bookmark.
In menu.
Restarted firefox.
Bookmark gone.
Disable Ubuntu Firefox Modifications 0.6.
Restarted firefox.
ALL extensions are now disabled.
Added bookmark.
In menu.
Restarted firefox.
Bookmark gone.
Quit firefox.
mv bookmarkbackups bookmarkbackups.bak
Start firefox.
Added bookmark.
In menu.
Restarted firefox.
Bookmark still there!
I also note that a new bookmarkbackups dir has been created.
Reenable all extensions (getting a bit tired of piecemeal step by step here...)
Restarted firefox.
Bookmark still there!

-- 
Firefox 3 Beta 5 not saving normal or live bookmarks
https://bugs.launchpad.net/bugs/225257
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