What version of the console are you trying out?
I've not seen this error in many years, so I'm a little stumped as to possible causes beyond a couple of vague possibilities; the most plausible situations I can come with for this are either:
a) the code that is trying to manipulate the boot sector is running into trouble with identifying the correct underlying physical disk device in Windows, or
b) some third-party thing like a piece of antivirus software is trying to block the Ghost management client from altering the partition table.
In years past there were a couple of other possibilities like INT13 drive overlays (although we did cope with most of those, too) but thankfully that kind of nasty hackery is behind us these days. Permissions are unlikely to be involved, since the management client should be installed as a service with the full permissions services have (running under the built-in LocalSystem account with the "act as part of the operating system" privilege).
If you're running GSS2, you can send me the ngctw32.log file from the affected client machine after this has happened and I'll see if I can narrow this down at all.
Edit: forgot the address, send it to nigel dot bree at gmail dot com