Hello there, Michal2975.
Currently, there's an open investigation regarding payments shown as pending in the Merchant Service Center. Rest assured this issue is taken with utmost urgency by our engineers.
We encourage all affected users to sign up to the list of affected users. This is to ensure you're in the loop on the progress of the investigation.
To get in touch with our chat support, click the following link and head to the QuickBooks Desktop with Payments section: Contact Payments or Point of Sale Support. Also, they're available from Monday-Friday 6:00 AM to 6:00 PM PT.
I've added an article that discusses in detail how the program groups all customer payments: Automatically record QuickBooks Payments bank deposits in QuickBooks Desktop.
We collated resources that will guide customers on how to handle any payments-related tasks: QuickBooks Payments FAQ. They're grouped according to topic so you can easily find the article.
Thank you for your patience while we're working on this. Feel free to visit the Community again if you have other QuickBooks concerns or questions about customer payments. I'm always ready to lend a helping hand.
