if you have removed all the virus corruption, double check with a online scan.
http://www.pandasoftware.com/actives..._principal.htm
reinstall 98 over it's self, as long as you dont format you wont have to reinstall anything, not even enter the product key, and all of your files will still be there. windows 98 seems to work better after a reinstall. when i used to load it on people's computers after i had everything the way i wanted it, i would reistall it over it's self and it just seemed alot more stable, so it really isnt a bad thing to have to do. this will fix your problem and save alot of hairpulling in the process.