I was working on an Operations Manager 2007 R2 deployment a while back where we had deployed the OpsMgr agent (including the Windows Server Operating System management pack) to a significant number of servers. One of the servers was a file server and we were looking for disk information on the system. Interestingly enough – that was the only server where we had none of the logical disk appear in Operations Manager. We debugged on the server itself, and on the RMS significantly and we validated that all other functions were working from Operations Manager. We also verified that drives were appearing for the same version of the operating system on different systems. The only exception was this specific server. We ended up opening a case with CSS and what they found was that there were some missing hotfixes which were required, and it was also required to make sure that the SYSTEM group has full permission to the drives (some drives on this server did not have this configured correctly). After applying the hotfixes and changing the drive permissions they appeared correctly within Operations Manager.

The hotfixes referenced were:

http://support.microsoft.com/kb/975928

http://support.microsoft.com/kb/970770

Summary: Missing disks on one of your servers? It may be an issue with VSS and disk permissions. Additionally see the hotfixes above.