During fragmentation, new fragments created are not considered in the displayed totals. For instance, this image shows that at 41% of the process there are no more fragments or fragmented files, but it hasn't completed:
The fragmented files at the top and end don't show up in the count displayed, even though they're obviously present (though they were created during the defrag process, so weren't discovered during the initial analysis). Here's my color mapping just to be complete:
I'm not complaining - I LOVE this program! Just want you to be aware someone else noticed.
Jim