Hi
 
> I ran a Clamav scan inside the Windows 2000 Vmware machine and it came
back clean --zero viruses-- whereas the external scan (of the vmdk file)
detected the virus!

This does not tell you, that the is no virus fragment left in unallocated
slack space in the virtual file system.
If the virus is there, clamav inside the VM cannot find it. However external
scanning can find it.

Maybe you can try  clamscan /dev/hda1  inside the VM to include slack space
for scanning.
(However, I have never done so and do not know about it's consequences. Do
at your own risk.)

Regards,
  Steffen

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