I noticed this too, and I've had to explicitly enable script debugging for each site. This can be done on the console tab where you have three checkboxes (off by default) for enabling Console logging, Script debugging, and Network monitoring. Or you can click the down arrow on the script tab and select Enable. I couldn't find any global setting to enable this by default on all sites or to save your settings. I have firefox set to clear all my personal info on each shut down, so maybe if you save your settings/personal info, this is persisted (I haven't tested this...just a guess).
I'm pretty sure this was done for performance reasons. Firebug would slow down JS-heavy sites (think GMail or Facebook) tremendously. In previous versions you could disable Firebug for particular sites, but now I'm guessing they changed it to be disabled by default because users couldn't figure it out and were complaining (and possibly uninstalling) for just this reason.