Can you check that in your custom code you have not overlayed any OOTB libs files ?
Similar issue was faced where below 2 files were overlayed, post merging both (latest libs file + custom code), parsys issue got resolved.
/libs/wcm/core/components/init/init.jsp
/libs/foundation/global.jsp
It should not be replicable in fresh AEM 6.4 instance, when we dont have any overlayed code.