Could it be that you’ve changed the mimeformat for SMTP? by default they are on both all (That would explain why for instance when u receive clear text it could not show up)
I only know the rule for POP but it might work on SMTP as well, please try and let me know (Im not at a site where there is a EX2k7 to test on and i didn’t got around to installing ex2k7 in VM on my notebook)
Get-casmailbox –identity User@E-maildomain –popmessagesretrievalmimeformat:0 |fl
I would start my search in that direction…
Also but probably stupid, try selecting all the text in the body it wouldn’t happen to show up then right?