I might have figured it out. Please point out with gusto if i haven't!
Go into your Account & Settings, select the option on the left for Sales, and look for the subsection Online Delivery. Your'll have "Additional Email Options for Invoices" set as "Online Invoice". If you change it to Plain Text, Save and send yourself a dummy invoice; does that show more as what you'd expect?
I suspect the Sales Receipt one is automatically sending as plain text, opposed to using the Online Invoice formatting. The customer would receive an email with the body of the email in plain text, and then the invoice attached. They'll still have the option to press on a big green View Invoice button, where they can be taken to the details of the invoice and further download/print copies for themselves.
Did the invoices previously used to be sent out as an attachment with a body email, or did your customers used to see the details of whats within your invoice within the body of their email?
Thanks Karsty! :)