The game generates the modifiers dynamically when you set up a league. The only tube it will reference the modifier files is when you create an exhibition game from the title screen.
If you are trying to get your league to play to the ratios of a particular season then you should select that season in the modifiers screen before opening day. Do not press the button to generate the modifiers. Simply select the season you want and then proceed to sinister until opening day and the game will dynamically create the appropriate modifiers to get the results you want.
There is no bug with the modifiers.
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