The game will always generate values based on a test sample. The values in the modifier file are averaged from some hundred or thousand trials of each season. However, any time something is adjusted in the game engine those files become relatively obsolete. Again, those files are really for exhibition games from the main menu. You should not ever need to press the auto calculate modifier button because the game will adjust the modifiers appropriately before opening day. It may be this stacking of calculations that is resulting in the strange values.
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