I can share some information about the about the issue you're getting in the QuickBooks Dashboard.
The issue with 940 payments still showing due after payment is made and form is filed is recently tagged this as an ongoing issue with QuickBooks Online Payroll.
Our engineers are already working to roll out a fix for this unexpected hitch. While they do, I'd recommend getting in touch with our QuickBooks Online Payroll Care Support so you're added to our notification lists of affected users. Here's how to contact us: https://payroll.intuit.com/support/contact/?infosrc=qs&service=64
You can have our representatives add you to the investigation number INV-24375. Once added, you'll get live notifications once an update is available.
Please feel free to get in touch with me if you need further assistance with QuickBooks. I'm always here to help!