Exactly, that's my issue with the Remote app on my iPad and iPhone. Now with the Remote app 3.0 and iTunes 11, all of my playlists, as they show up in the Remote app, are not sorted the same as they are on my screen in iTunes.
The sort order in the Remote app seems to be by the far left column in iTunes... the Manual "number of the song" column in Ascending order only. Very frustrating. With the playlist in iTunes sorted by that far left column ascending, I can drag a song to a different position and that song DOES move to that exact position in the Remote app on my iPhone; that works. But if you want to sort by ANY OTHER COLUMN, forget it, the playlist order in the Remote app does not match what's on the screen in iTunes.
Sorting is apparently only by the far left Manual column, ascending order. I usually like things sorted by the Date Added in most of my iTunes playlists, so all my recent stuff is at the top. I want to see the same sort order of songs in the Remote app as I do on the screen in my playlists in iTunes. It used to be seamless before this "upgrade."