you could reset that to default and make sure it's the cause, before 'fixing' it
i'm not sure if that would cuase it... also, go to each league's "stats and ai" page.. that's where that checkbox is located for each individual league... maybe, for some reason the independent leagues aren't included, accidentally or purposefully, not sure why it wouldn't.
stats locking should be more machine-like in results.. even if talent ebbs and flows. i guess if a ton of players ented the league at some point, and it doesnt adjust mid-step? i think it's more of a continuously applied operation/procedure, though. could be wrong. based on how much it slows simming down, it's doing some heavy lifting compared to simply simming.