Let's get to the bottom of this, jenslight.

I'd like to get more information though. What transactions are duplicated? Invoices or payments?

With regard to the paid and closed statuses, the Closed status applies to the payment transaction, while the Paid status applies to the invoice when it's paid in full. 

Refer to the screenshot.

You can always go back to this thread if you have further information or if you have further questions. You can also mention me so I can get back to you personally. Have a great one!