SyncTunes selects iTunes playlists using their name, the one you see in iTunes. As such this means that the playlist's name must be unique with iTunes, otherwise the wrong playlist may be selected. Additionally, this also applies to iTunes playlists that are within iTunes folder playlists. For example:

This may cause a problem if you selected to sync the iTunes folder 'Mobile':

• Mobile
  • Rock
  • Shuffle
  • Audiobooks
• Current Favs
  • Newly added
  • Shuffle
  • 4 Plus Stars

The wrong 'Shuffle' playlist might be used by SyncTunes.