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When first creating a game, there's an option under the Player Options heading in the Game Options tab: "Keep career posts. stats". The options are to "Keep all", "Major Leagues only", or "Keep none". After creating a league, you'll want Game Setup -> Player & Picture Options to find the setting.
If set to "Major Leagues only", the game will likely keep the postseason stats for minor league teams long enough to finish the playoffs, then get rid of them. This likely never follows over to the Player Profile.
Does that solve your problem?
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