You generally see this issue when the VM is powered on. To get around this in NFS datastores, scan inside the .snapshot. On VMFS, you might be able to create a VM snapshot, then scan the -flat.vmdk (mileage may vary).
Sorry Tom, I was thinking of the workaround for mbrscan. The reason for the warning in this case is that if you align the virtual disk, then apply the delta (from the snapshot), you'll have a corrupt guest. While there are uses for a scan, it might not be required. For example; If you know the Administrator did not take the steps required to align the VM prior to installing the guest and the guest OS is legacy Windows (XP, 2k, 2k3), its not aligned.