The issue with Plain Text has been present in all recent versions of OSX and Mail. In Lion, it is only the inability to assure Plain Text that is problematic. In earlier versions of OSX and Mail, if only one font and color of font was used, Mail automatically changed to use Plain Text. That is gone.
I would need to examine the Raw Source of mesages sent from these different SMTP to understand what would be different, and that could be an important difference if the case.
In the case of the Sent mailbox issue, I have determined that if a message with attachment is composed and Sent in Snow Leopard with Mail 4.5, say, and the account is IMAP, then in Lion and Mail 5.x the message can be seen in the same account's Sent mailbox in a proper manner. Likewise, the message sent from Mail 5.x will be seen to be in proper form when viewed in the same Sent mailbox via Mail 4.5 in Snow Leopard.
There is much to learn about this latter, odd, issue.
Ernie