So we are experiencing the same issue for the last several days.  When we send invoices, the email is not formatted correctly with the email template that we chose.  It adds Intuit Turbotax, Credit Karma, Quickbooks, & MailChimp icons at the top and bottom.  It includes a "Hope to See You Again" message and a "Do you have an Issue" message at the bottom of the email.  We found out today that if we turn off all the payment credit card options in the invoice, the email will format correctly.  Unfortunately, it doesn't have any of the payment links.  If we turn these options back on, then the email will format incorrectly.  I've tried this with both the Online Invoice setting enabled and also set it as HTML.  We use Intuit Quickbooks as our credit card processor.  For us, this appears to be an issue with the payment links altering the email and pulling in its own template.  It's a bug that needs to be fixed by Quickbooks.