Is there a scripts.rpa file in your game folder? Make sure you delete it, if so. Other than that, are you overwriting all the files that want to be overwritten?
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I am having the same issue on my Mac. I tried it on the 1-11 free version and the 9-11 Elysium version and it only brings 1-11 when the game is booted. as far as "scripts.rpa" files to delete (not sure which one) there are three 3 Elysium_scripts.rpa endurance_scritps.rpa and game_scripts.rpa. It seems to be replacing necessary files otherwise but brings up the same version.