Tim:
We've seen plenty of plain text message parts being transcoded in transit by some allegedly "helpful" mail server (turning quoted printable into 8-bit, etc.). I wouldn't be the slightest bit surprised at a mail server doing the same sort of thing to text/html content.
Patrick O'Callaghan:
Quite, but the OP says it all works properly if he sticks to TB. Even allowing for the difference between inline PGP and PGP/MIME, it would seem particularly perverse of the intermediate server to mess with one and not the other. But I guess stranger things have happened ...
But one client might be using a different content encoding scheme, by default. The original poster can easily test this by writing a message in each, then looking at the raw message kept in their sent mail folder, before any external mail server has a chance to alter it.