I had typed this long post with screenshots, then when I went to submit it I learned I could only use three URLs. I put the whole story with screenshots on a rudimentary web page. Please don't laugh at it, I'm not a developer and I don't even dabble in code or HTML or whatever.
The web page with all of the details is here: https://sites.google.com/view/digitalvolcanohelp
Short version:
I ran the tool using search criteria: same content, all file types; scan location Yes to both scan against and Yes uniques on the smaller data set that I want to rid of uniques. I got a huge number of uniques, and no duplicates. However, I know that there are duplicates.
I ran it again with scan against off, getting the same results.
I ran a subset of the data to confirm that I know there are duplicates. There definitely are:
With the smaller data set, I switched to audio mode. I got more duplicates listed, but I still had false uniques.
I'm desperate and don't know what else to do. Please help me!