Yes, it makes sense, is Apple changed how Mail displays HTML. Maybe that's how the new version works and there is no option to control it. However, keep in mind that how the message looks to YOU does not necessarily change how the message looks to your recipient. It could very well be that, with either the Jaguar or Panther version of Mail, the HTML was being sent as an attachment, and whether or not it displayed "inline" (within the body) was and is determined by your recipient's e-mail client, not by how it looks on YOUR screen.
Said another way, in case I'm not saying this clearly: When a message includes an e-mail attachment, the e-mail client can display it inline or not. Mail may have changed how it handles outgoing mail with HTML, and we know for sure that it now gives you an option about how to handle incoming mail with HTML. How it looks to people receiving your mail is up to their e-mail client, not yours.