I am pretty sure this new 4.1 bug is related to an age old bug: Apple breaks Smart Playlists on iPhone and iTunes alike (yet again).
Some podcasts referenced in smart playlists won't sync to my iPhone after the 4.1 update. If I force them to sync by manually adding them to another list they appear in the smart playlist, but they appear in the wrong order. They appear first.
Looks like Apple doesn't understand the Smart Playlist bug. They fixed part of it, and broken another part.