Hi,
1. If the "shipping invoice" option is activated, the "shipping invoice" button you see in the backend when you edit an order will use the PDF invoice plugin. If not, it will use the normal display. The shipping invoice is never sent in the email notifications. Usually that's something you want to print physically to add in the package that you send via the shipping carrier.
2. In the "statuses for email attachment" you entered "shipped" instead of "confirmed,shipped". So the invoice will only be added to the email notification if the status of the order is "shipped", which is normally not the case when the email notification is sent just after the payment as the status is normally "confirmed". So you probably want to revert that to "confirmed,shipped" and it should work like before.