OK, so I was having the same problem, essentially. Finally, after reading this thread, and unsuccessfuly attempting to fix it, I managed to get it working. Here's what I did:
(I'm not sure that all of these steps were necessary, but this is it anyway)
1. Turned off iTunes Match on the iPhone. I know that this is scary for some of the people here, so I'm not sure that this will be all that helpful. If not, I'm sorry.
2. Quit iTunes.
3. Restarted iTunes.
4. Clicked iPhone.
5. Clicked on Music.
6. Clicked on Selected playlists, artists, etc. in the top Sync Music box.
7. Selected playlists, artists, whatever.
8. Clicked Sync at the bottom.
9. Everything worked. I think. I haven't been able to check everything, since I added a LOT of music. But what I have looked at is indeed where it is supposed to be.
I hope this helped at least someone.