Hi again,
Sorry for the slow reply been gone all weekend. Well if you haven't already done so please run the scan with system restore off. I don't think this will make a difference since it said that the full scan is "malfunctioning", but this is the procedure that we usually try to follow. If that doesn't work there are other options that I can think of. Some are easier than others depending on what resources you have at yoru disposal.
1. If this is a networked computer try using anther computer with sep installed on to run the scan of the infected computers harddrive.
2. If you have another hard drive to boot from then slave the infected drive and boot off of the other drive. Then run the scan on the infected drive. This is similar to the networked option above.
3. You can make (or if you call in I think we can provide a link for download) a bootable cd that runs a scan off the system without ever even touching the drive. That way you know 100% that any infection isn't altering the scan. This sort of cd isn't officially supported but I have had very good luck with it thus far. Basic instructions for making it are below, and if you have any questions feel free to pm me.
1. Get WinPE (instructions here:
http://apcmag.com/windows_pe_20_a_tiny_version_of_windows_for_system_maintenance.htm)
2. Download and update Norton Security Scanner(NSS)
3. Copy the NSS folder on the WinPE CD/USB
4. Boot the infected machine using the WinPE live cd or usb stick
5. Browse to NSS folder and run nss.exe too to scan and clean the infected machine.
Hope this helps,
Grant