sounds to me you have something weird going on, try this:
first turn off system restore , this will have you lose your previous restore point, but in all reality, when system restore does it's thing, it also restores the virus too, so turning it off, will leave no where for the trojan to hide.
next do you know the name of the trojan, for example: trojan23.exe
if so, then you can put in the name into your search browser for a fix for it.
if not, then try a free on-line anti-virus scan at housecall
, you can use this if you have a fast connection, i would not use if you have dial-up.