Use Beyond Compare to verify. It quickly surfaces file system differences in a nice GUI.
Side By Side Directory Comparison
The directory comparision displays a side-by-side listing of the "source" and "compare to" directories. Use the "<>" option to display only the differences:
Line by Line File Comparision
Differences will be highlighted via color codes. When you want to drill down into a specific file difference, simply double-click to view a line-by-line file comparison:
Use the referee icon to enable/disable compare options. For instance, an extract from Visual Sourcesafe will yield a new date/time stamp, even if you know the file on the compare directory is identical. Unflagging the "Timestamp" folder comparison criteria will remove this comparison "noise" and allow you to spot more meaningful differences.