Hi,
WOW, It has been a very long time but I have finally got back to the investigation of this MFT vs File System Scanner issue. Take a look at http://mftscanner.codeplex.com . The new version will write all the files in lower case, sorted order so that a tool such as WinMerge can show you the differences.
I think the code is quite optimized (mostly) and most MFT open/dumping can be achieved in less than a few seconds. This is very promising, but I'd love to know why there are differences in the numbers of files reported on System type folders.
Cheers.