I have always upgraded FF by logging in as root and launching the browser and selecting the Check for Updates under the Help menu within the browser. I have upgraded my VL6 Classic to FF 3.6.3 this way, however it killed my java plugin. However after upgrading to jre 6u18 with Gslapt, my java plugin is back. BTW i had to enable the testing repo in Gslapt to get the updated jre.
Does the new FF package include the java plugin? Because if not it will most likely break it.