Get a second opinion, since there's lots of false positives nowadays. Fprot has a decent free antivirus, and MacAfee has an online virus scan called House Call or something like that. You can also shop at BitTorrent, if you know what I mean.
Go into your registry (Start - Run - regedit.exe), go to (if i remember correctly) HKeys Local Machine - Software - Microsoft - Windows - Current Version - Run and then look for strange things in there. Be careful, check the directories they're in. They often name themselves things that sound legitimate. In Win98 you don't need hardly anything in there. I had 2 or 3 things at most on my Win98 (everything else is just bloat that slows you down). Also check Run Once, and Run Service, whatever it's called. Delete entries out of there, it controls what loads on startup. Find the virus files the registry says is loading on startup and delete them. Reboot, and see if they come back. Google whatever you know about the viruses (name, directory, symptoms, etc.) and the virus guys will have more help for you there. You can back up your registry by (I think) "exporting" to a file before you make changes, and if you mess it up, just double click the file and it will reset it back.
p.s. I no longer use Windows, I have a Mac and I also run Ubuntu Linux and OpenBSD. *Every* operating system is better than Windows if your software will run on it or you're willing to switch software. I HIGHLY recommend switching if it's at all possible.