Dependency bundle ignored by SystemJs

I am trying to get my angular application to the point where it is ready for distribution and I have managed to create 2 bundles, one for my angular application and one for my dependencies (which include the angular framework and the rxjs framework). Both bundles are produced and my custom bundle (which contains my code) is loaded by the front end but the vendor/dependency bundle is ignored and the dependencies are still loaded from the node_modules folder.

My solution is based mostly on this previous answer on Stack Overflow with a couple of exceptions like not including/inlining my html templates and adding node_modules to the exclusion path of the dependencies.

I will include everything I believe is relevant to the problem, if more is needed please let me know. I'm thinking that it is an issue with my dist-system-config.js file that I use in the final distribution, I am sure there is something I just do not fully understand.

I have also created a question on Stack Overflow. Any pointers would be very much appreciated.

What I have observed:

The 2 bundles are generated. The file app.bundle.js is 12KB in size. The file dependencies.bundle.js is 773KB in size.
Both bundles are found and loaded by the browser, I can open them both from the browsers dev. console under sources (I am using Chrome for testing)
In the browsers development console output I see the angular and rxjs scripts still being loaded from the node_modules folder. primary issue
In the browsers development console output I do not see my application files being loaded which is expected (they are being loaded from the created bundle)
The angular application loads the expected component on the screen

Index.html

<!DOCTYPE html>
<html lang="en">
<head>
    <script>document.write('<base href="/" />');</script>
    <meta charset="utf-8"/>
    <title>Test bed</title>
</head>
<body>

<RootComponent>Loading content...</RootComponent>

<script src="/node_modules/core-js/client/shim.min.js"></script>
<script src="/node_modules/zone.js/dist/zone.min.js"></script>
<script src="/node_modules/reflect-metadata/Reflect.js"></script>
<script src="/node_modules/systemjs/dist/system.js"></script>

<script src="/bundles/dependencies.bundle.js"></script>
<script src="/bundles/app.bundle.js"></script>
<script src="/Scripts/dist-system-config.js"></script>

<script>
    System.import('app/boot').catch(function(err) {
        console.error(err);
    });
</script>
</body>
</html>

app/boot.ts

import { platformBrowserDynamic } from '@angular/platform-browser-dynamic';
import { enableProdMode } from '@angular/core';
import { AppModule } from './app.module';

enableProdMode();
const platform = platformBrowserDynamic();
platform.bootstrapModule(AppModule);

Scripts/dist-system-config.js

System.config({
    baseURL: '/',
    paths: {
        'npm:': 'node_modules/'
    },
    map: {
        'app': 'dist/app',

        // angular bundles
        '@angular/core': 'npm:@angular/core/bundles/core.umd.min.js',
        '@angular/common': 'npm:@angular/common/bundles/common.umd.min.js',
        '@angular/compiler': 'npm:@angular/compiler/bundles/compiler.umd.min.js',
        '@angular/platform-browser': 'npm:@angular/platform-browser/bundles/platform-browser.umd.min.js',
        '@angular/platform-browser-dynamic': 'npm:@angular/platform-browser-dynamic/bundles/platform-browser-dynamic.umd.min.js',
        '@angular/http': 'npm:@angular/http/bundles/http.umd.min.js',
        '@angular/router': 'npm:@angular/router/bundles/router.umd.min.js',
        '@angular/forms': 'npm:@angular/forms/bundles/forms.umd.min.js',
        'rxjs': 'npm:rxjs'
    },
    packages: {
        'app': { main: './boot.js', defaultExtension: 'js' },
        'rxjs': { defaultExtension: 'js' }
    }
});

gulpfile.js

var gulp = require('gulp'),
    tsc = require('gulp-typescript'),
    Builder = require('systemjs-builder');

gulp.task('bundle', ['bundle-app', 'bundle-dependencies'], function(){});

gulp.task('app-components', function () {
    return gulp.src('Scripts/app/**/*.ts')
        .pipe(tsc({
            "target": 'es5',
            "module": 'commonjs',
            "moduleResolution": 'node',
            "lib": [ 'es2015', 'dom', 'es2015.iterable' ],
            "sourceMap": true,
            "emitDecoratorMetadata": true,
            "experimentalDecorators": true,
            "removeComments": true,
            "noImplicitAny": false
        }))
        .pipe(gulp.dest('dist/app'));
});

gulp.task('bundle-app', ['app-components'], function() {
    // optional constructor options
    // sets the baseURL and loads the configuration file
    var builder = new Builder('', 'Scripts/dist-system-config.js');

    return builder
        .bundle('dist/app/**/* - [node_modules/@angular/**/*.js] - [node_modules/rxjs/**/*.js]', 'bundles/app.bundle.js', { minify: true})
        .then(function() {
            console.log('Build complete');
        })
        .catch(function(err) {
            console.log('Build error');
            console.log(err);
        });
});

gulp.task('bundle-dependencies', ['app-components'], function() {
    // optional constructor options
    // sets the baseURL and loads the configuration file
    var builder = new Builder('', 'Scripts/dist-system-config.js');

    return builder
        .bundle('dist/app/**/*.js - [dist/app/**/*.js]', 'bundles/dependencies.bundle.js', { minify: true})
        .then(function() {
            console.log('Build complete');
        })
        .catch(function(err) {
            console.log('Build error');
            console.log(err);
        });
});

package.json (Relevant versions only)

"@angular/***": "4.2.6",
"canonical-path": "0.0.2",
"gulp": "3.9.1",
"gulp-typescript": "^3.2.0",
"rimraf": "2.6.1",
"rxjs": "5.4.2",
"systemjs": "0.20.14",
"systemjs-builder": "0.16.9",
"typescript": "2.4.1",

systemjs / builder

Dependency bundle ignored by SystemJs #819