What exactly is this trojan/anti-virus doing?
I had one at the office the other day. McAfee couldn't do a thing about it. Malware stuff saw it, but could do nothing. It would recreate its file everytime something tried to quarantine or delete it. Same for the startup entry. Deleting the entry manually, and immediately it would come back. It also hides itself in the task manager. However, it was dumb enough on recreating the file to not check the actual contents. I just replaced the file with a zero sized file (just copy over a zero size file or open the bugger in notepad and ctrl-A, DEL, ctrl-S it), rebooted and removed startup entry since the thing could now no longer run.
If this trojan you have is doing the same thing then find the related file and empty it, but don't delete it and reboot. That's if you don't have a CD-based solution and want to do it while Windows is running. And don't sit with the PC connected to the 'net while you're trying to clean it.