Some of those trojans create registry entries that you have to manully remove... do you remember the name of the trojan that was found? The scanner usually says what it is, and also gives urls for more info on it. If it was IRCbounce, then this thread
gives you some info on registry, and if it was vbs_moon.k, the trend housecall site i gave in last post has info on the entries that one makes. Sadly, there are others as well. You really NEED to remove it completely, including the registry entires. Just be really careful editing in the registry, i always suggest doing a backup first.