Hi there,
I have run into a similar issue where after performing a scripted build of Windows 2012 R2 Standard (and then running Sysprep to prepare to dump an image) the "File:\windows\system32\config\system status 0xc000000f (registry) error has appeared. After many hours of testing I was able to locate the cause for our particular instance.
The culprit was indeed the Altiris (Ghost) agent, but it was not the agent installed on the W2K12R2 OS, but the agent that was run previously in the WinPE PXE image that we use for the OS deployment. The agent in the WinPE Bootdisk was configured to log to the following path ; "C:\Windows\Temp\DAgent\DAgent.log" - this is the default settings for the Ghost agent in the WinPE3.1 bootdisk. Now because we didn't wipe the contents of the HD before installing the OS, the windows W2K12R2 install picked up this existing file\folder and renamed it to : "C:\Windows.old\Windows\Temp\DAgent\DAgent.log".
For some reason the existence of the "Windows.old" folder and file caused issues with Sysprep (even though it never produced errors during the Sysprep run) and caused the Black Screen 0xc000000f at the next reboot.
My fix was to edit the agent.inp file for the Altiris agent in the Bootdisk and disabled the clinet logging. The Windows.old folder was then not created during the OS install and Syprep susequently ran fine and the OS rebooted successfully!
Hope this helps someone out there...