I've noticed that many invoices that have originally been set up as Direct Debits, fail to process as Direct Debits and switch back to manual payment method.

My GoCardless is correctly integrated with Quickbooks so there are no issues on that end. Just in case, I have already approached GoCardless with this and they have assured me that there is no issue on their end. When I create an invoice I check to make sure that the Direct Debit option is ticked off. However many times I've realised that the payment is still overdue for a long period on these invoices, so when I open up the invoice to check what the problem might be, it has reverted back to the manual payment method (let customer pay by card). I'm not sure why this is happening but it is causing issues as I'm not getting paid from customers in time. Can anyone help?