Why do my most recent iTunes music purchases not sync to my iPhone?
I had this exact same problem and found the answer I was looking for within one of the Apple communities. Simply go into iTunes store and scroll right to the very bottom. There amongst the small print you'll see an option for purchased. Click on there and you will see a list of all songs/albums and you can choose to either download all or individual tracks. Once downloaded they appear in your library as normal. Don't ask me why they don't appear straight away, but this resolves the problem of those not transferring when syncing