Thanks for the reply, Adam.
I do't think I explained myself very well - sorry!
The issue I'm seeing relates specifically to the Setup > Invoicing > Email > Default Subject & Message text. The text I have entered here, both for Invoices and Statements, had not been changed, but this month's invoice runs sent out a default message that was missing the line breaks, so that all the text I entered in the Message field is populated in the email body as one big block of text, and the formatting with respect to line breaks is ignored.
I have since tried to delete the message text and re-enter it, and I still see the same problem.
Best,
Darren