I think I worked out what was going on here.
The problem was I had already created the invoice, then edited the master style to make a new custom invoice template. I went back in to the invoice and applied the new template to the invoice using the 'customize' option at the bottom of the screen. When you do that, it picks up most of the new template, but it doesn't pick up the 'message to customer' field.
But it works fine when creating new invoices going forwards. So I deleted the invoice and re-created it from scratch. The 'message to customer' field is then populated correctly, so all working fine now!
