I am experiencing the same thing.

When using Winmerge I have it eliminating identical file but there are a whole bunch of files that are showing up as different when they are not. They appear to be core files that I have never touched but I can't feel comfortable with that.

Fortunately I was pretty good about using the override but would like to know why identical files are showing up as different.

I get to this part of the upgrade file and get all crazy because I have a whole lot of identical files to look at. What do I do?