I've set up Stripe payment in test mode and have it working in eCommerce.  The payment is correctly linked to the invoice.  In the portal, the payment works (i.e. from the portal users standpoint the transaction is successful) but it is not linked to the invoice or Sales Order. I see the eCommerce payment in Accounting->Sales->Payments, but not the portal payment.

When I look at Accounting->Configuration->Payment Transactions I see both eCommerce and Portal payments.  The eCommerce are already linked to the correct Sales Order, the portal are not.   Even after editing the portal payment and linking it to the Sales Order (which is linked to the invoice) the payment is still not recognized on the invoice or the customer.

I am using Stripe, but I think this is a problem with other payment providers.