RequireJs: module path does not exist error in build with r.js

I'm making use of RequireJs, and I'm having trouble with the build.

My structure is

webroot
  css
    /* css here */
  files
  img
  js
    emails
      verify.js
    lib
      jquery-1.8.3.min.js
      jquery-ui.min.js
      jquery.ui.selectmenu.js
      modernizr.js
      require.js
    orders
      form.js
    common.js
  js-build
    /* expected build output here */
  js-tools
    app.build.js

This is a part of a CakePHP project, but the webroot is where the actual webroot of the web server will be.

node and r.js.cmd are both on my path, so I haven't included it in the js-tools directory.

When accessing the default page, the is /, but it could also appear as /orders/form. For this reason, relative Urls to the JS is an issue.

When I load the JS, I'm using

<script type="text/javascript" src="/js/lib/require.js"></script>
<script type="text/javascript">
//<![CDATA[
require(['/js/common.js'], function(common){
    require(['orders/form']);
});

//]]>
</script>

This is taken from https://github.com/requirejs/example-multipage-shim.

My common.js is

requirejs.config({
    "baseUrl": "/js/lib",
    "paths": {
        "orders": "../orders",
        "emails": "../emails",
        "jquery": [
            "//ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min",
            "jquery-1.8.3.min"
        ],
        "jquery-ui": [
            "//ajax.googleapis.com/ajax/libs/jqueryui/1.9.2/jquery-ui.min",
            "jquery-ui.min"
        ]
    },
    "shim": {
        "jquery.ui.selectmenu": ["jquery", "jquery-ui"]
    }
});

As it stands, this works when working with unoptimized code. The important feature is that js is referenced with an absolute URL, is it can be picked up by the code from either /, or /orders/form.

My app.build.js is

({
    appDir: '..', /* relative to app.build.js */
    mainConfigFile: '../js/common.js', /* relative to app.build.js */
    baseUrl: 'js/lib', /* relative to current directory */
    dir: '../js-build', /* relative to app.build.js */
    optimize: 'uglify2',
    paths: {
        "jquery": "empty:",
        "jquery-ui": "empty:",
        "jquery.ui.selectmenu": "empty:",
        "common": "../common",
        "orders": "../orders",
        "emails": "../emails"
    },
    modules: [
        {
            name: 'common',
            include: [
                'modernizr'
            ],
            exclude: ['jquery-1.8.3.min', 'jquery-ui.min', 'jquery.ui.selectmenu']
        },
        {
            name: 'orders/form',
            exclude: ['common', 'jquery.ui.selectmenu']
        },
        {
            name: 'emails/verify',
            exclude: ['common', 'jquery.ui.selectmenu']
        }
     ]
})

When optimization runs as r.js.cmd -o js-tools\app.build.js from the webroot, I get a js-build directory with a copy of the whole webroot directory, optimized. Although not ideal (I wanted to limit it to just the js directory getting optimized), I can use my Ant driven build script to copy the contents of the js-build\js directory to the correct location.

When I run the build from the command line, the generated common.js, orders/form.js and emails/verify.js all exclude jquery.ui.selectmenu. common.js has modernizr included, as well as the header from the same lib. form.js and verify.js also exclude jquery.ui.selectmenu, and are devoid of any headers.

However, when I run from my Ant script, orders/form.js and emails/verify.js include jquery.ui.selectmenu and modernizr, even though I've given specific instruction for common and jquery.ui.selectmenu to be excluded.

I've excluded jquery.ui.selectmenu, because the particular version I am working with is written the the following form, and the browser has an issue with the end jQuery variable not being available. By excluding jquery.ui.selectmenu, I can attempt to load it separately, as though it came from a CDN.

(function($, undefined) {
    $.widget("ui.selectmenu", {...
    });
}( jQuery ));

So, my issue is, how come the same app.build.js is resulting in different output?