The virus has probably corrupted some of your files or there are pieces of the virus remaining. Might be a good idea to try running a scan with a bootable AV Rescue disk to verify that all of it is indeed gone.
Free Bootable AntiVirus Rescue CDs Download List
(Kaspersky has been known to cause problems in the past, if they have remedied this, I do not know, so you may wish to try one of the other disks)
After scanning, you should run a SFC to try to restore the integrity of the files.
SFC /SCANNOW Command - System File Checker