I'm using Samsung Galaxy Note 2 and been having this issue with both the original Android 4.1 and current 4.3. Happens using native Music Player and Musicmatch.
I synchronize playlists using Windows Media Player, playlists and music get copied to the device and work fine. After a while, frequently when I reboot the phone, the playlists disappear, but the music is still there, however, the only way I have to get the playlists back is to delete all the songs manually and sync again. If I just try to sync the playlists without deleting the songs the playlists are copied but they are empty (they are not associated with the existing songs in the phone despite that they are on the same folders).
Any clue as to why the playlists disappear or how to resolve appreciated.