I ran NPE normally. NPE indicated it needed to reboot to perform it's magic, I allowed NPE to do that, it rebooted and ran. NPE did not report any issues and claimed to have not made any changes.
I then tried to reboot into Ubuntu Linux. The Grub screen came up, I choose Ubuntu, it started but then hung part way into booting Ubuntu Linux. Several attempts at booting Ubuntu hung at the same point.
From Grub, the system boots into Windows 7, just not into Ubuntu.
So it appears that NPE did something to the boot system that interfered with Ubuntu being able to boot.