Had the same problem, took me hours to find the solution.
You just need to create the script’s object using the iframe’s document.
var myIframe = document.getElementById("myIframeId");
var script = myIframe.contentWindow.document.createElement("script");
script.type = "text/javascript";
script.src = src;
myIframe.contentWindow.document.body.appendChild(script);
Works like a charm!