The way that I got Widget Options to work for my custom post type "treatments" and to show all the terms under by custom taxonomy "conditions" was to modify some system files (hopefully at some point these files can be moved into the theme or my custom style).

First I added my code to the display.php file found in warp --> systems --> wordpress --> config --> layouts --> fields

Here is the code in my display.php file:

<?php  
/**  
* @package   Warp Theme Framework  
* @author    YOOtheme http://www.yootheme.com  
* @copyright Copyright (C) YOOtheme GmbH  
* @license   http://www.gnu.org/licenses/gpl.html GNU/GPL  
*/  

    $options  = array();  
    $defaults = array(  
        '*'          => 'All',  
        'front_page' => 'Frontpage',  
        'home'       => 'Home (Posts page)',  
        'archive-treatments' => 'Treatments Archives',  
        'taxonomy-conditions' => 'Conditions Archives',  
        'archive'    => 'Archive',  
        'search'     => 'Search',  
        'single'     => 'Single',  
        'single-treatments'     => 'Treatments Single',  
        'page'      => 'Pages',  
    );  

    $selected = is_array($value) ? $value : array('*');  

    if (count($selected) > 1 && in_array('*', $selected)) {  
        $selected = array('*');  
    }  

    // set default options  
    foreach ($defaults as $val => $label) {  
        $attributes = in_array($val, $selected) ? array('value' => $val, 'selected' => 'selected') : array('value' => $val);  
        $options[]  = sprintf('<option %s />%s</option>', $control->attributes($attributes), $label);  
    }  

    // set pages  
    if ($pages = get_pages()) {  
        $options[] = '<optgroup label="Pages">';  

        foreach ($pages as $page) {  
            $val        = 'page-'.$page->ID;  
            $attributes = in_array($val, $selected) ? array('value' => $val, 'selected' => 'selected') : array('value' => $val);  
            $options[]  = sprintf('<option %s />%s</option>', $control->attributes($attributes), $page->post_title);  
        }  

        $options[] = '</optgroup>';                    
    }  

    // set categories  
    if ($categories = get_categories()) {  
        $options[] = '<optgroup label="Categories">';  

        foreach ($categories as $category) {  
            $val        = 'cat-'.$category->cat_ID;  
            $attributes = in_array($val, $selected) ? array('value' => $val, 'selected' => 'selected') : array('value' => $val);  
            $options[]  = sprintf('<option %s />%s</option>', $control->attributes($attributes), $category->cat_name);  
        }  

        $options[] = '</optgroup>';                    
    }  

    // set conditions  
    if ($terms = get_terms('conditions')) {  
        $options[] = '<optgroup label="Conditions">';  

        foreach ( $terms as $term ) {  
            $val        =  'tax-'.$term->slug;  
            $attributes = in_array($val, $selected) ? array('value' => $val, 'selected' => 'selected') : array('value' => $val);  
            $options[]  = sprintf('<option %s />%s</option>', $control->attributes($attributes), $term->name);  
        }  

        $options[] = '</optgroup>';                    
    }  


?>  
<select name="<?php echo $name;?>[]" style="width:220px;height:120px;" multiple="multiple">  
    <?php echo implode("", $options); ?>  
</select>

Next I modified system.php in warp --> systems --> wordpress --> helpers. This is my code.

/*  
        Function: getQuery  
            Get current query information  

        Returns:  
            Object  
    */  
    public function getQuery() {  
        global $wp_query;  

        // create, if not set  
        if (empty($this->query)) {  

            // init vars  
            $obj   = $wp_query->get_queried_object();  
            $query = array();  

            // find current page type  
            foreach (array('home', 'front_page', 'archive', 'taxonomy-conditions', 'archive-treatments', 'single-treatments', 'search', 'single', 'page', 'category', 'conditions') as $type) {  
                if (call_user_func('is_'.$type)) {  
                    $query[] = $type;  

                    if ((is_single()) && (get_post_type() == 'treatments')) {  
                         $query[] = 'single-treatments';  
                     }  

                    if ((is_archive()) && get_taxonomy( 'conditions')) {  
                         $query[] =  'taxonomy-conditions';  
                    }       

                    if ((is_archive()) && is_post_type_archive( 'treatments')) {  
                         $query[] =  'archive-treatments';     
                    }  
                    if ($type == 'page') {  
                        $query[] = 'page-'.$obj->ID;  
                    }  

                    if ($type == 'category') {  
                        $query[] = 'cat-'.$obj->cat_ID;  
                    }  

                    if (is_tax( 'conditions')){  
                        $query[] = 'tax-'.$obj->slug;  
                    }  


    }  
            }  

            $this->query = $query;  
        }  

        return $this->query;  
    }  

The end result is that I have widget options for my templates as well as all the terms in the custom taxonomy "conditions."

Again, I hope this helps.