How are you “rerunning” the script? If you just make new selections in Dynamo without closing the file, then Dynamo will just update the current graph rather than create new instances. This is intentional. You either need to close the file before creating anything new or you need to run the script through Dynamo Player where this will happen automatically.
If you’re doing either one of these things and the elements still get replaced, then you’re dealing with element binding.