To see if the theory of a misconfigured server is correct, is there a log we can check to see which server we download from? Maybe by IP address if they are not doing any reverse proxying?
Chris_UPW, you might want to take a look at Fidelity's Cash Mgt Account (CMA) with free checking, and a 2% cash-back credit card, which you can setup to auto-deposit the cash back into your CMA. They work well with Quicken. Keep your Chase savings account in case you need to deposit a bunch of cash, since Fido's not a bank.
It has been at least a week without any duplicate downloaded transactions. This coincides with the time I updated Quicken to version 36.38. It appears the infrastructure update used to connect Quicken to financial institutions, making it more secure and reliable may be helping. Fingers crossed.