Ren'Py games keep persistent data but it shouldn't really effect a new game. The things that are saved outside actual save games is usually gallery stuff and viewed dialogue for skipping purposes.hmm Are the error messages normal? Or is it conflicting with some files left over from the previous versions? Does the game store stuff anywhere else other than the game folder? I'm pretty sure it must because I didn't keep my old saves but it still finds them somehow...
If you want to know where saves are kept here's a link:
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