I have a scenario where my starting RB is maybe playing the first snap, then barely plays the rest of the game. My backup ends up playing basically every snap from then on. I also overrided it so that my FB doesn't play in certain formations, but they still hand the ball off to him. My fatigue setting is set to 1 for RBs. Has anyone else encountered this situation?

That is the lowest setting which will play the backups the most. Set it above 40 for RBs and both of those guys should see 50% to 70% of the snaps. Anything below 30 will have starting RBs playing less than the back ups