I don't know why this is not the very first line at the top of doubleTwist:

"Important to remember if you want to add a new playlist, or a playlist with altered content to your phone without wiping all the other playlists - or taking the time to resync already happily existing playlists. Remember: drag and drop is cumulative. Syncing is a total do-over."

So, I have re-synced twice to get all the content on there since I was unaware of this little rule.  On a positive note, doubleTwist is free, easy and seems to covert files to usable media on any device where many other programs fail.