Hmm, haven't heard of this before. Did you have anything like NoScript, etc installed in Firefox? (you really, really should have)
Also it sounds like you may want to change your antivirus (& software firewall if you don't have a physical one) to a more effective one, or at least ensure it's updating properly, seeing as it required you purposefully running a scan to pick up nastiness being installed onto your machine, rather than detecting it coming over the wires/running/being written to disk.
In any case, if it actually "cleaned"/"removed"/"quarantined"/whatever the trojan*, it could be that an important firefox system file has been hosed by the incident and the clean up. Uninstall it and re-install the browser, then try again. And for the love of god get yourself a better secondary other than IE - Opera, Chrome, etc. And some kind of secondary spyware/etc checker and cleaner, like Spybot SD or HijackThis.
If you find you can't shut down after cleaning and uninstalling, just kill the power and hope none of your system files have gone. I think windows may have a system file checker you can use before shutdown but i can't for the life of me remember what it's called or how to use it as in 5+ years of using XP and more under 98 (which i think introed it), i've never had to.
* or should I say _suspected_ trojan - the rather sensitive Kaspersky AV we use at work decided that Google Maps Streetview was trojaned yesterday and killed my browser tab. Could be that one of the convoluted link addresses it generated looked like malicious code? In any case, it managed to pick up that Explosm was under attack last week before their frontpage even properly loaded. That's hardcore.
EDIT - wow as i was typing that everyone said pretty much the same thing
