XML Schema support was updated in IS 7.1.x. I did not review your attachment, but if it contained recursive references or other rarely used but valid XML definitions not supported in IS 6.5, that could explain the difference.
My recommendation is to use your XSD to create an IS schema in IS 6.5. IF that works, write your own Flow to create and send a valid request message. The Flow generated by the Web Services Connector is nothing special, use it as a pattern only.
If you can not create an IS schema from your XSD, there is likely something there that is not supported in IS 6.5. You can refactor that in the schema so long as an equivalent instance document can be created and added to your outgoing soap request.
Mark
#API-Management#webMethods#soa