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one file i know that is prone to it is rsilvers filament drive. me and a few others have gotten the s3d bug with it. you run it through netfabb and it says it all ok. if open it up though in rhino and try to save it again it gives me a warning that it has an error. there is obviously something more to a model than being manifold and closed. something thats very slight but makes s3d go nuts.