I was able to get rid of the extra data sources by closing them and republishing to my test project. I have also removed my local copies to clean up my environment. I republished the original data source after editing it by itself using your method above and verifying I returned the same number of results.
However, I'm still having the same issue, not that it's a show stopper, but it's my OCD that I want to solve this.
In this screenshot of the problem child connection, you can see that it references back to itself.
If I click on the 'connects to' name, it shows this, which is the correct db:
This is the other workbook that is behaving correctly. All of this I pulled directly from Server and nothing from my machine.