RT6 form and payment was submitted electronically. I received notice that it was Rejected but not explanation as to why. The payment went through.

Knowing why the RT6 form and payment were rejected is important so you can make the necessary changes and fix them, cherbert.

When the tax agency declines the RT6 form and payment you've submitted, they'll email you the exact reason for the rejection. If you haven't already, please check your spam or junk folder. They may have sent another email that explains the reason for the rejection.
 

If you don't see any, you can contact our Payroll Team. They can check your account and give you an accurate reason since you've submitted it electronically. 

Another option is to work with the IRS or your state agency to get the exact reason and necessary details to take action based on the reason for the rejection. 

Still, you can refer to the bullets below to see the possible reasons for form and payment rejections:
 

• Duplicate tax filing
• The account number is invalid or correct
• The form was sent too early 
• Tax deposit or filing schedule is incorrect

You can visit this page to learn more about handling payroll e-file and e-pay rejections: Tax form and E-Payment Rejection.

Lastly, you can read through this article for tips about managing the status of your tax forms/payments and payroll reports:

•  View the status of your payroll tax filing. 
•  Run payroll reports in QuickBooks Online Payroll. 

Be sure to post again if you have follow-up concerns about tax forms  and payments in QuickBooks Online Payroll. I'll make sure to help you further.