JS files added to template.php not being aggregated

API page: https://api.drupal.org/api/drupal/includes%21common.inc/function/drupal_...

In my theme template.php I have a number of files that I add using drupal_add_js. When aggregation is turned on, these files do not get captured. If they are supposed to appear in a aggregated "JS_THEME" file, all that is there are semi-colons (;).

In this example below, these files should get aggregated but they are gone and just 2 semi-colons are there. I actually have a larger number of files and have tried them one by one, two at a time, all of them etc. They do not ever appear in a aggregated file. I have tried using preprocess => true and cache => true. They do not aggregate so I have to use preprocess=>false on each one when aggregation is turned on otherwise they're gone.

function wkh5_preprocess_html(&$variables) {
drupal_add_js('/sites/all/themes/mytheme/js/iframe-resize.js', 
array(
  'type' => 'file',
  'group' => JS_THEME,
  'weight' => 1,
)
);
drupal_add_js('/sites/all/themes/mytheme/js/mytheme-js.js', 
array(
  'type' => 'file',
  'group' => JS_THEME,
  'weight' => 2,
)
);
}

My scripts are only partially updated and I am wondering if the nomenclature for using the behavioral stuff (Drupal.behaviors.exampleModule = { attach: function (context, settings) { etc etc) is required.

Example of my script function syntaxes (all are wrapped up this way):

jQuery(function($) {
  $('#dongle .head').click(function() {
    $(this).next().toggle('slow');
    return false;
  }).next().hide();
});

The scripts/functions I am using all work fine, they just do not aggregate anything but a semi-colon for each script. The preprocess_html function wraps up a number of drupal_add_js & drupal_add_css files (7 css, 6 js)... none of them get aggregated.

Where am I going wrong? Does this issue belong here?...