I've noticed this with my Galaxy Nexus, I think it is a problem with MTP support in Ubuntu. With regard to the question I sync my Galaxy Nexus with Synx which doesn't work great but it gets the job done.I use the built in Rhythmbox player with my Nexus S rooted running 4.2.1. My method: You have to make sure there is at least one mp3 file on the device, in the music folder. RB recognizes it as a 14gb filesystem and a media player, but when I click the media player it gives me a notice that it cannot connect, the 14gb filesystem is still showing though. If you right click on the device the choose sync with library a window pops up with a box at the top, if you click the little subdir arrow you can choose which playlist sync. When you connect the device later it will remember which playlists/songs synced under this menu. It saves all the music in my music folder with dirtree music/artist/album/song while the playlists always appear in my root directory as .pls files. so far the playlists have all been recognized by all my music players (apollo/amazonmp3/aolplay/googleplaymusic/esmediaplayer). Back when I had a win system I was using songbird which getdeb has a version of, I'm not sure how well it works though.