I'm having the same problem. I've emptied Safari's cache, and tried player 4 and 5 settings in the tab editor. I have player-licensed5.swf everywhere it's supposed to be, I believe, including in the plug_cbplayeradvanced folder. Yet the logo persists. I'm not seeing it when I use a JW module on my site, or if I insert a video with JCE which uses JW as the player. I'm at a loss here.
Update: If I click the play button in the middle of the video, the logo doesn't show up. If I click the video title (same video) in the playlist, the logo DOES show up. Weird.