Two things from your screenshot.
Your Subject line is blank. Worth filling in regardless of the body issue — a remittance arriving with no subject tends to look like spam at the vendor's end.
On the body itself, the greyed-out Body field is expected; the rich text editor underneath it is the input, and that's where your text should go. Since it's there, the question is whether the setting is on the node that's actually being used at run time.
Which level did you configure this at — module, vendor account, or the specific transaction? And is it on the Original node or a Copy? Print management inherits down the hierarchy, so a setting made at one level gets bypassed if there's an override further down. The PDF would still generate either way, which fits what you're seeing.
Also worth knowing how you're sending — from the payment journal, or through a batch. That changes which path the email takes.
