It's possible that the two drives were cloned in the past (or are virtual containers) and have the same Volume Serial Number (VolumeID) and signature. Duplicate Cleaner uses this to check if two paths are mapped to the same place to avoid false duplicates.
It is possible to change a drive's volume ID if you are confident doing this.
I hope to get an update out very soon (next week probably) which allows you to skip this check.