I was able to figure out what was causing the issue.
It’s actually similar to this issue that was reported:
https://www-secure.symantec.com/connect/forums/32-bit-ghostwalker-and-bartpe-usb-drive
What happens is the volumes are automatically added (which can easily go unnoticed). Also it doesn’t say anywhere that other volumes can’t be included.
If you pay close attention to the update of the SID when these volumes are added, it runs through it and then brings you back to a command prompt. No message or error. I was assuming at first that meant it was successful and also didn’t notice that when running with the /batch switch. What it was actually doing is running the registry part of the update on the OS partition and then hitting the other volumes and fail without an error. Hence only partly updating the SID on the OS partition.
The reason I figured this out is because I tried it on another computer that had a dual boot it worked, but I had to select the OS because it detected more, but it didn’t auto select any other volumes.
Windows 7 creates a 100 MB partition usually. Also Dell and many other manufacturers have a diagnostic or recovery partition. Any of these will cause it to fail. In Windows 7 this will cause a temporary profile to be loaded for all users. Also whatever implications could be present with only part of a SIDs are updated.
In Windows XP it also fails and doesn’t report it. The downside is in windows it reports no errors. This could cause long term issues since half of the SIDs are not updated and would be really hard to diagnose.
I still say this is a bug because it doesn’t show an error and I don’t believe it should auto select other volumes.
I will be using the /AV=None switch to only do the OS partition. (Note: The value of None only works in newer versions. Couldn't find it documented, but it works.)