Log files are being updated constantly, and in fact the VSS snapshots that Windows creates for backing up the drive doesn't actually include all of the data on the drive. The trick when comparing Windows partitions though is that many changes will be EXPECTED. And you may not need this capability for this particular purpose, but if your right-click any given file (or folder), you can choose to copy one side's version to the other in order to quickly resolve differences that shouldn't exist. You can also use the View to menu to individually show or hide files that are identical, files that are different, or files that only exist on one side or the other. At that point you'll have a single folder tree to drill into, and differences between each side's versions will be highlighted along the way.

To do this, make sure you choose a 'Full Contents' compare, and then when you get the results (be patient), in order to view them more effectively I recommend going to the View menu and enabling Tree Mode. But WinMerge can do that sort of comparison. But for this sort of comparison, you'd probably want a comparison to compare the full bits of the files by hashing them rather than just checking for differences in size and/or Date Modified timestamps, and that can take QUITE a long time if you want to do it for an entire drive's worth of files. You can compare a 'live' system to a mounted image or two mounted images to each other. I use a freeware tool called WinMerge to perform these sorts of comparisons.

Winmerge vss