I wonder if this is related to the bug I found sync'ing playlists to Rekordbox on my iPhone. Are your playlists with problems Intelligent Playlists that are set up to match "all of the" listed conditions and also use My Tags? If so, it could be the same problem (see my post today).
My workaround for the mobile sync bug is to remove criteria based on My Tags from the Intelligent Playlist definition.