If you had viruses on it, you could have very well have some damaged system files. At times files get renamed or replaced with virus files, and the scanner removes them.
First you should scan the drive with a second anti-virus utility to cross-check things. Avira Antivir is good, and has a boot CD you can download, all free. Then run a malware scan using Malwarebytes. Download and install it, reboot the PC in Safe Mode with Networking, and run a Full scan. This all will take a few hours.
Then make sure XP is up-to-date with patches, on SP3, run Windows Update, then try again.