Do you have SP2?
Do you have the Windows XP Installation cd with SP2?
What did you use to scan for malware?
I suggest you try Windows Onecare free scan
Windows One Care Free Scan
Using Internet Explorer go to Windows Live Onecare Free Scan.
It will say "Get a free PC safety scan"http://safety.live.com/site/en-us/default.htm
Make sure you click "Full Service Scan"
in the middle of the page and not the "Try It Now Free" on the right side.
Allow it to download an Active X component.
Choose "Complete Scan" in the window that opens
Do not click on anything else that offers you a free trial or to sign up if you live in the US.
Allow it to scan - it may take quite, maybe two hours or so depending on how big your hard drive is and how fragmented your registry and drive are.
After the scan completes, reboot and try your floppy and cd again.