Thank you for taking the time to visit the Community to post your issue, although I apologize that you haven't received a response.
At this time I would recommend contacting support directly for advanced troubleshooting steps.
https://www.quicken.com/support#contact-support
Quicken Care has the tools to initiate a screen share to view the issue in real-time.
Thank you,
-Quicken Tyka
drsmith said: Sometimes if I download and import transactions manually, it will clear things up and I can reconcile, but I have to do it one account at a time.