There are some occasions it won't let you put stuff it's found into the virus vault.
If it finds something in the recycle bin, then you'll have to empty it. It might report the trojan's location as "Recycler", but emptying the recycle bin is a good start.
It might find stuff in a restore point which it won't be able to get rid of. To get rid of these, temporarily turn off System Restore, see
here for instructions on how to do this. Don't forget to turn it back on!
I found that it would report some cached Java stuff as containing viruses. The only thing I could do in this case is track the file (usually a zip file) and manually delete it.