Could you email me the files "HKLM_1.txt", "HKU_1.txt", "files_1.txt", "HKLM_2.txt", "HKU_2.txt" and "files_2.txt" so I can try to investigate? I realize the files are rather big, but zip'ing (or rar'ing or 7z'ing etc) should help a lot.
I don't think the behavior is related to a security application though, but I guess you never really know...
My guess it's a brainfart on my part in the comparison-code --- something that should be fixed in the upcoming version as the comparison code (amount other things) have been completely rewritten. I can make no promises as to when the upcoming version will be released, though.