I've encountered similar problems on my new SE and 9.3.1. After syncing first time, many songs missing -- plus for some reason by default the first song always replays unless I manually reset. When I resynced, the replay issue got resolved but a few albums still missing all the tracks???

Being new to 9.x., I assumed it's just some bug that will eventually be fixed.

In the meantime, google play is my backup! ^