i would say that the trojan is still lurking somewhere, i would take out the hhd, make it a slave by moving the jumper on it, then putting it in a freinds computer, and have him/her scan it with their anti-virus. if nothing found then..
if you have a spare hhd, i would load a fresh copy of windows on there / install a anti-virus that has at least a 30-day trial period / ...then put in the hhd with the trojan on it, and scan it with the new anti-virus. also make sure the hhd with the trojan on it, is set to a slave drive.