What about if files are referenced? If they line up, try turning off True Scale and see if a ratio appears on one of the two scale factors. That would indicate some type of working units issue.
We also sometimes have labeled grid coordinates in two files using grid lock with a 50' grid unit and compared how not only do the files align but how the grid coordinates align.
We also sometimes have labeled grid coordinates in two files using grid lock with a 50' grid unit and compared how not only do the files align but how the grid coordinates align.