I know it is not very helpful to this discussion, but I have had unexplained behavior with this tool, as well. It sometimes just doesn't set all the settings that it's supposed to; sometimes, I can run it a second time, and -- poof -- all the settings will be correctly set that second time.
Over 50% of the time, it will get it the first time. Sometimes, I have to run it twice. Rarely, I have to run it three times.
For us, the settings that don't seem to take as well are the wake-on-LAN and PXE-on-wake settings.