I have the exact same problem, and havent been able to find a solution so far. Actually, the issue is more global, as NOTHING synchronizes but the content I had in my backup. The weird thing is that after i restored from my backup, the tracks did were in my iPhone, but didn't appear in the "Music" app. Since then, i have managed to manually delete them, and i can export tracks to my iPhone if in "manual mode". Better than nothing, but it doesn't solve our problem.