WYSIWYG CKEditor config.js not being used?
This took some research, but I found this article which describes how to do it.

The meat of the article is the following hook, which defines a custom config file:

&lt;?php
/**
 * Implements hook_wysiwyg_editor_settings_alter()
 */
function MODULENAME_wysiwyg_editor_settings_alter(&amp;$settings, $context)
{
    // The $context variable contains information about the wysiwyg profile we're using
    // In this case we just need to check that the editor being used is ckeditor
    if ($context['profile']-&gt;editor == 'ckeditor')
    {

        // The $settings variable contains all the config options ckeditor uses. 
        // The array keys correspond directly with any setting that can be applied 
        // to CKEditor - as outlined in the CKEditor docs: 
        // http://docs.cksource.com/ckeditor_api/symbols/CKEDITOR.config.html 
        // Another way to override configuration is to use your own configuration javascript
        // file. In this case, we're going to add our own configuration file that will
        // Hold our stylesSet customizations... 
        $settings['customConfig'] = base_path() . drupal_get_path('module', 'MODULENAME') . '/ckeditor_custom_config.js';
    }
}