I have run into this a couple of times since joining.
What I discovered is if you toggle between Allstar and Rookie and back again at the top of the Set Lineup page, it comes up with all the players when you get back.
Give that a try and let me know. It cost me a vital game a few seasons ago before I stumbled across this combination, and the same thing happened to a friend of mine when he started as well and this combination worked for him as well.