But you had Team Chemistry on, right? I think the rookie MPG problem is worse with Team Chemistry on and Player Roles off, because without Player Roles everyone is happy, which means every team has 100% chemistry, which means every player in the league gets an unrealistic attributes boost. Because of that, the CPU won't play rookies much because the guys already on the team are rated far better due to the boost from high chemistry.
If you turn Chemistry off, you will see rookies play a pretty realistic amount of minutes.
With Player Roles and Team Chemistry OFF, I don't see any of the symptoms of the big man glitch — neither simulated nor during gameplay. The guys that should stay around the paint do so.