Interesting Virus on Vista Makes Files and Folders Disappear

My usually very-dependable but very-slow Compaq Presario computer (SR5250NX) got hit by a nasty virus this weekend.

Symptoms, as narrated by my wife, were system reports of memory problems and the disappearance of all folders from the desktop, My Documents, and other places.

I ran a Knoppix LiveCD and found all the folders still there, and backed them all up with an external Hard Drive, so nothing lost, apparently.

A manual run of AVG showed that all of these "lost" files and folders were there, but inaccessible to the scanning software, which gave the message "Locked File. Not Tested."

Something had clearly changed the status of these files and folders, so after restarting in "Safe Mode" (hit F8 while computer reboots) I ran a battery of malware and antivirus programs, including

Microsoft Windows Malicious Software Removal Tool
Superantispyware
Malwarebytes' Anti-Malware
Hijack This
Zone Alarm
Microsoft Security Essentials (the new Microsoft antivirus program)

They turned up a few likely suspects, but I'm not sure if I've got the virus completely yet.

The computer is behaving as normal again, but the folders all remain hidden. I've had to go into the "folder options" of the Control Panel and select "show hidden files and folders" (etc.).

Yup, everything is still there, but listed as "read only" and "hidden". I hope that this is the only lasting effect of the virus. I guess I'll have to find all the files and folders that the virus altered, change their settings back to normal, and hope that nothing worse has been done.

Fingers crossed.