You are missing that I did do that and when I clicked from manual to auto sync I tunes deleted all the playlists I had just created and worked on. In fact It Locked up 3 times in the 2 hours I was working on my stuff. That's what you missed.
I've never heard of that before, never know anyone to create a play-list and then it deletes them all the second you try to sync together.
The only thing i can think of is if your iPhone wasn't connected to your account/library from your iPhone...