Helios Comms I actually noticed this behavior before also. I used to use Free File Sync, a similar file copy/sync tool between machines. I had to stop using it because after each copy it would start a whole batch upload to OneDrive again. It's been a while and I forget the exact sync scenario I had setup, but my findings were exactly the same as yours. I actually never looked into why it was happening. I ended up adding the OneDrive client to each machine I was originally syncing manually. Then I just added everything to the OneDrive folder that I specifically wanted to sync between those machines and the cloud. This solved the issue of using a program to manually sync between them.
So there is definitely something that gets tacked or modified on to the file post upload.