I have a HostOS with 4x GuestOS's, some with physical VMdisks.
The HostOS was recently rebooted but when it came back up it ran CHKDSK which found 'problems' on one of the SAN disks (which is piped thru to one VM). It then deleted all the Security IDs it didnt recognise and replaces them with "default" Security IDs which are different to the original NTFS permission sets.
2x Microsoft articles describe this Q831374 and Q913034. I have contacted Microsoft and applied hotfix KB263628 to my Win2003 SP1 HostOS and GuestOS. But it didnt fix it.
I have invetsigated further and found that I can only apply perms to the GuestOS if I also apply perms to the same disk at the HostOS. However another GuestOS owns 3x VM physical disks and works just fine.
I have also just applied 4x Microsoft Updates: KB920213, KB923980, KB890830 and KB922760. I have removed KB922760 - though it seems totally irrelevant. After that and meddling with NTFS permissions it seems to be working ok. I suspect resetting all the perms is what has doen the trick and I have zero faith in it not happening again.