Perhaps I'm not understanding the issue.
It's not overwriting the files, it's creating -new- ones.
When you disable "allow existing files to be replaced" MB will copy the existing filename and add an underscore (_) and a number after the filename.
Every file in your screenshot has this. So these files already exist, but you told MB not to replace them so it's creating new ones. The "new filename" column is showing you that.
Filename_2.mp3 means you already had -two- of that track.
Filename_3.mp3 means you already had -three- of that track.