I noticed this sync problem recently when I just happened to notice that one of my playlists on my iPhone 5 had the wrong number of tracks. Then when I looked, of course, I realised that so did ALL of them, sometimes as few as half the right number.
As to the cause, that's not clear, especially as the ios7 upgrade, new iTunes and, in my case, a replacement phone becuase of a fault on the power switch, all happened at around the same time.
As for a solution, I was fumbling around with all the ones on offer here before a couple of days ago when I took the plunge and did a full restore (with c.11000 tracks to go back onto the phone bumped down to 128k I was reluctant to do this unless absolutely necessary). As 7.0.4 had just been released I restored and then let the new version go on before I put my back up on. Then I added my playlists one by one and checked the track numbers each time. As I have one playlist that then adds around 8000 tracks at random from my library, I left that until last.
So far, fingers crossed, everything is back to where it should be; I have all the playlists, they are all the right number of tracks and a couple of new albums I've added this morning have synced correctly. We'll see if this lasts, but of course I can't now tell if the restore did the trick or the 7.0.4 update.
Unless it was the update this really is unacceptable from Apple. Music is the cornerstone of what they provide and a simple thing thing like syncing correctly is absolutely essential. Let's hope this is the end of it.
Edit - just remembered - I also had an aborted attempt at using Match just before the issues started. I had to get a refund from Apple as my library wouldn't completely upload (that's another story) but I did wonder if that was part of the problem?