Just coming back to this thread as I had the same problem again, this time with iOS 7.1. It's the most frustrating thing having to restore and manually resync over 7,000 songs.
I've finally come to the conclusion that its an iTunes issue as I had this problem once with iOS 6. I've since changed to MediaMonkey to manage my iPod touch and so far, it hasn't let me down. Music is syncing as it should, when I want it to. If I only want to add one or two songs, I just drag them from the library in MediaMonkey to the iPod and its transferred in about 2 seconds.
I agree iTunes has an issue, I had to manually sync, hopefully it will be fixed soon.