I recently was asked about the file system issue with Windows and thought I would be a little more in depth. The file system problem is resolved with the following patches:
MS831375 and MS873437 for Windows 2000
Here is a good description of the problem (3rd paragraph down) and Microsoft’s page.
Basically when a large volume has over 4,194,303 files a flaw in the chkdsk utility run in fix mode or repair mode can strip the permissions from the files. Patch MS873437 is related. Here is the link.
MS831374 is for Windows 2003 and is the same issue with the chkdsk utility.
According to our administrators we had systems on other patch reboots go into the chkdsk utility and automatically start running in fix or repair mode. So in our case it was not something that was user initiated. Hope this helps and have fun patching!