You shure you didn`t use any aditional mods that don`t include in the gwx ?

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Do you have expirience any problems with your pc (not only in sh3 i mean)?
Maybe the GWX download files are corupted some how - that the option, also try to delete the game save directory from (my documents\sh3) try to delete all the folder and then run the game (don`t worry it will automaticly create a new one instead).
I hope that will help you some how :hmm: