I currently have a case open on this, and he's checking into the "why" aspect of this, but I thought I'd post here too.
The 2003 Operating System MP (version 6.0.6667.0) has a Mount Point discovery rule in it. (The 2008 MP probably does too, but I don't have a 2008 server with mount points.) Anyway, the disks that were being used as mount points were never being discovered. It turns out that the script the discovery rule runs (Microsoft.Windows.Server.MountPointDiscovery.ModuleType.vbs) requires that the mount point have a LABEL!
Set WMISet = WMIGetInstance("winmgmts:\\" + sTargetComputer + "\root\cimv2", "win32_volume where drivetype=3 and driveletter = null and label <> null")
Now, why the discovery is checking for a label, I don't know. Once I gave one of my mount points a label, it discovered it, and everything worked fine. Does anyone know the reasoning behind checking for a label? Maybe everyone else makes sure their mount points have labels, and I'm the exception.
If nothing else, I thought I'd post it here for future reference, in case it helps someone else out.