I have had this same issue for almost 2 years as well.  I have to manually add deposits as nearly all of them do not post when using the merchant deposits function.  The invoices are marked paid and that is it.

Hello there, ihaveanopinion.

I can see how the automatic payment deposit feature allows you to work with customer payment efficiently. Hence, let me route you to the appropriate support to get the help you need with your concern.

Since you've mentioned that the issue regarding the inability to deposit payments automatically has been going on for almost two years, I recommend contacting our Payment Support team. They can thoroughly check your account and determine the most appropriate resolution. They can also raise a ticket to get this investigated when necessary.

Here's how:

1. Visit this page: Chat with us.
2. Fill in all the needed information.
3. Click on Start Chat.

You can also visit this article to locate their contact details under the QuickBooks Desktop with Payments section if you need further assistance: Contact Payments Support.

On the other hand, consider scanning these materials for guidance on reviewing transactions, deposits, and fees using your Online Service Center or on dealing with delayed deposits:

• Why is my batch deposit delayed or suspended?
• Find transactions, deposits, or fees in the Merchant Service Center

Keep us posted if you have additional questions regarding the automatic payment deposit or other related concerns in QuickBooks Desktop. We're here to help.