I was going to go into great gory detail about the problems I had with Firefox 2 that it turned out were related to the tabbrowser preferences 1.3.1 extension, until I wandered over to http://forums.mozillazine.org/index.php and noticed that there seem to be a number of different problems with that extension when using Firefox 2. So, to cut down on your trial and error debugging, if you’ve just switched to Firefox 2 and notice weird problems, as a first step try disabling the tabbrowser preferences extension if you have it.
In my particular case, it was interfering with loading links that start with java script:openwindowOld, but I see from mozillazine that it’s causing a few different problems.