Noticed a difference in the MIME headers, maybe this has something to
do with it?

When a send the message via desktop mail client it uses "Content-
Transfer-Encoding: quoted-printable" and this is the message that
works properly.

However, when relaying via Google Apps it is using "Content-Transfer-
Encoding: 7bit" with "Content-Disposition: inline" and this is the
message that doesn't display any of the disclaimer stuff in the text/
html version.