Hey Nicolas,
You're correct.
When I change the status to anything in the backend, the order number is included.
We are using the PayPal plugin. It works fine - but the email that is triggered once the order is paid, is the one I included here - WITHOUT the order number.
I guess I'm confused though - because when paypal triggers the email (changing the status from created to confirmed), the email that is sent, not only does not include the order number, it also has a different font as the h2. Is it possible it's pulling from a different email template?