Basically you need to make your changes with PM, then generate the MD5 hash, and then never modify the file again with PM (or any other program) and then the MD5 should no longer change. If your system is generating the MD5 hash before PM makes changes (or any other metadata-savvy app does) then the hash will change.
I'd really need to have a diagram of your system in order to help you solve this problem.
I
THINK I'm making all the changes with PM. I use PM to ingest, create directories, rename files, and once they are all ingested they do not get touched. After all the files are uploaded I organize the directories, move them to the "import" directory on the laptop, and import them into their proprietary processing tool where they are scaled to a common size, compressed, and uploaded to their file servers.
I'm just guessing but I think the duplicates may have been me reingesting a card and using a different set of IPTC data which would mean a different directory created, filename, and IPTC data which, I assume, would provide a different MD5 hash that they same image already ingested.
I just explained to them what was happening and if they have time to waste humoring this one small cog in the system I'll setup a test event and do it without IPTC data being added to the images, and, just to be safe, without renaming the files.
Mike