You say it's only specific players. What does the game say is his recommended role? That field is to the middle right of the main player screen IIRC. I'm guessing it just doesn't feel he's good enough to be a starter.
Alternatively, I wonder if it may have something to do with your 7-day lineups.
I thought that if you just had them empty then it would automatically use the set rotation mode, but I was wrong. You have to select no to using 7-day lineups.