The problem is the game is using the individual position player/pitcher limits to override the overall setting. So if you set that to 4 or whatever, but leave the player/pitcher limits to "no limits," it ignores the other.
I posted about this issue when I noticed it in my Japanese league where I set the limit to 4, but both pos. player and pitcher to 3 so they had have at least one of both to use all 4 spots. Instead they got 3 of each. (battists responded to my thread pointing out it was an issue.)
At the moment you have to set individual limits for it to work properly.
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