This thing has been driving me absolutely crazy for the last three months. I tried nearly all of the suggestions here. Managing music on my iPhone manually seemed to work best, but yesterday it started making problems, too. Besides it's not very comfortable to do this manually. That's why you use Apple, because everything is running smoothly and automatically, don't you?
So I decided to try one last thing and deleted my whole iTunes Library and imported all my music to iTunes again and then synced it with my iphone. When it asked if I really wanted to sync with this unknown iTunes Library I was a bit afraid, I would have to download and configure all my apps again, but they remained the same. And for the music...
So far it is really working!! 🙂 🙂 🙂
I synced about ten times yesterday and today to see if the problem reoccurs, but everything seems fine. I lost all my ratings for the songs, but I don't care as long as I can plug in my iPhone again without the fear of having (nearly) no music on it afterwards. So I guess (at least in my case) it was some error in the iTunes Library.