Did you ever find a solution to this? I have spent some time in the settings and am disappointed. It was one of my favorite features with this phone/spotify. I am considering changing to a different cover because I use it all the time.
Not sure if its related to this issue or not, but I have found that the Spotify controls will only show up properly on the S-View screen when Spotify does not have focus (i.e. when you unlock/open the cover, Spotify isn't open). If Spotify is open and you close the screen, the controls appear for a second or so and then it disappears again.