Why is an invoice with SEPA payment following a different dunning schedule?

If you are seeing invoices with SEPA payment method follow a different dunning schedule, this is expected behavior. 

Per our Adyen documentation, "Invoices paid for with an asynchronous payment method that enter dunning must also be treated differently than invoices paid for with a synchronous payment method." Since SEPA is an asynchronous payment method, it follows the same schedule as PayPal eChecks and you will therefore see a totally different schedule followed as well as different invoice statuses throughout the dunning cycle.

The description here (under PayPal eChecks and Recurly Dunning and Retries) shows the sequence of events and what happens in each step to the invoice and transaction.