For a while (it might have started in the days of Intrepid/Kubuntu 8.10) my Thunderbird window never remembered its geometry between restarts. When starting TB, I always got a small window which I then had to resize to the desired size. No changes to prefs.js seemed to make a difference. Today, I came across a post which pointed me into the right direction. On Jaunty (Kubuntu 9.04), I had to do the following: Open System Settings, click on Window Behaviour in the section Look & Feel.
Fix Non-persistent Window Size for Thunderbird