No actually the problem is that in 1.0.12 we look for the podcast shortcode, and if it's found, we assume that the player is already taken care of. If you put the URL in the middle (this is a pre WordPress 1.5 behavior), we don't process that, because we assume it's handled by the shortcode, but then on the opposite situation, the shortcode isn't processed correctly because it's using a pre WP 1.5 logic.
We're removing the podcast shortcode check, which means PowerPress will still add it's player to the top/bottom of posts, and the shortcode is still processed when stand-alone. Essentially, the next update will fix your problem, though not perfectly. Anywhere you used [podcast]http://www.example.com/path/to/media.mp3[/podcast], the shortcode will be removed, and then PowerPress will add it's player and links either above/below your posts. If you just enter [podcast] without the URL, PowerPress will put the player and links in that position.