I'm not sure how I accomplished it (probably because I am uber clever!) but I have 2 versions of FF.
that executes from /usr/lib/firefox/firefox and one
Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.9.1) Gecko/20090624 Firefox/3.5
that executes from ../lib/firefox-3.5.3/firefox.sh
Mozilla/5.0 (X11; U; Linux i686; en-US; rv:188.8.131.52) Gecko/20090910 Ubuntu/9.04 (jaunty) Shiretoko/3.5.3
The first one has all the extensions, themes, bookmarks etc. that I use all the time, but the other one is the one that's automatically updated through Synaptic.
How do I make the later version adopt the profile from the earlier one? Then I can remove the one that doesn't update.