go into safe mode and do another scan. chances are the trojan may be running but it's unable to kill it because it's running (you what windows is like when you're trying to delete files in use/running). in safe mode, nothing's running, so it won't have that problem.
viruses in quarantine are safe. hence why it's called quarantine. the virus-riddled files are stored in some encrypted fashion which ensures they can't be executed, nor decrypted by a virus's counterpart app or something. most viruses that i know of/have come across, come in 2 pieces. these ones are harder to get rid of, because one copy looks after the other, and vice versa. stop one running, the other one restarts it. delete the file before the 2nd, the other will clone and re-start it. generally speaking, the *only* way to get rid of these is in safe mode, when neither copy are running. then it can delete both of them.
i always run a virus scan in safe mode if i know i'm dealing with one. makes detection and removal a lot easier.
what's a better thing to do, is to go here http://www.trendmicro.com/download/dcs.asp and download sysclean. create a directory or something on your c:\ drive to copy all this into, because it all extracts itself into about 15 files (plus the pattern files). so keep it all together. then download this http://www.trendmicro.com/ftp/products/tsc/cpr/tsc.zip into the same directory, and extract. before rebooting into safe mode, download and install this too http://www.download.com/Ad-Aware-2008/3000-8022_4-10045910.html?tag=mncol.
now go into safe mode and run the sysclean.com file (.com is a weird .exe). it'll extract into a dos prompt box, then launch a nice window. press "scan now" and leave it do it's thing. if anything is left over that your normal av didn't pick up, this will sort it out. then before going back into normal mode, run adaware.

this is a tried and tested technique i used many many times when i was a field engineer. i would execute this process more or less religiously if i was to ever encounter a virus, and it worked pretty much every time. i can only recall once when it didn't work, but there were exceptional circumstances to that one, to which i won't bore you with.
hth.