I had this same issue and was able to resolve it by commenting some code out. As
todotoit mentioned above it seems to be related to using plugins, I was using Draggable. To resolve I made a copy of Draggable and commented out the very last function (export to AMD/RequireJS and CommonJS/Node) - starting at line 2291. you can see in that code there is some requires which i think Electron is confused about the file structure... removing this did the trick for me and was able to run the project finally:
//export to AMD/RequireJS and CommonJS/Node (precursor to full modular build system coming at a later date)
// (function(name) {
// "use strict";
// var getGlobal = function() {
// return (_gsScope.GreenSockGlobals || _gsScope)[name];
// };
// if (typeof(define) === "function" && define.amd) { //AMD
// define(["TweenLite", "CSSPlugin"], getGlobal);
// } else if (typeof(module) !== "undefined" && module.exports) { //node
// require("../TweenLite.js");
// require("../plugins/CSSPlugin.js");
// module.exports = getGlobal();
// }
// }("Draggable"));