I'm also seeing weird sync issues since upgrading to iOS 7. The sync issues started when I first upgraded to iOS 7 so I suspect that iOS 7 is to blame and the other system differences aren't an issue (i.e. I also upgraded to Windows 8.1 but it never worked properly when I was on Windows 8). For me, the only way to "sync" all the smart playlists and music is to restore from backup and then the first sync seems to work. However, I haven't tried that recently (I tried it a month back or so and it worked then) because it is ridiculous to have to restore your phone just to sync things! Apple needs to fix the iOS 7 quality issues.