If you can send (as attachment) the original message source, I could see if maybe there is a bug in Aqua.
Should also mention that I have code on my side to detect UTF-8 no matter what the encoding in the message says.
Finally, if you were seeing this in a Gmail account, with message headers (not content) --
-- Gmail's IMAP irreversibly corrupts non-ASCII characters in message headers. The IMAP spec says they're allowed to.