As to the USB Auto setting: when you reset your player or reapply firmware, the USB setting resets to Auto; you just need to remember to reset the setting to what you are using. (Also, the USB setting has no effect on the player’s playback–the USB setting affects the computer protocol under which the player will connect to your computer.)
Not sure why your music is not showing on your player. Is the music of a type compatible with the Clip?
Will your player still play? If so, a sometimes fix-all solution is to reformat the player under its settings–but note, this will delete your content on the player. Before trying that, first try a reset: hold the on button down for 20-30 seconds (and some people report needing 60 seconds or more for this).
If the player ultimately will start and will connect to your computer, I’d also try reapplying the latest firmware–it could have become corrupted.
Good luck!
