FYI, new free tool from Microsoft just released that can be used as a full system (file system, registry, ACLs, etc.) diff'er:
http://go.microsoft.com/?linkid=9758398

I've added it to CRCETL @ http://www.woodmann.com/collaborative/tools/Attack_Surface_Analyzer

Nice, thanks for the heads up and CRCETL submission. (and sorry for the late reply)