The following code is not saving to the appropriate taxonomies (or anywhere). When the post-type is opened in wordpress, the fields are back to their default, and none of the taxonomy boxes are checked.

It is saved in “meta-boxes”
The first two fields are the issue.

/*
Title: Recipe Particulars
Post Type: gw-recipe
*/

piklist( 'field', array(
      'type' => 'select'
      ,'field' => 'gw-cuisine'
      ,'scope' => 'taxonomy'
      ,'label' => 'Choose Cuisine Type'
      ,'columns' => 4
      ,'choices' => array(
        'american' => 'American'
        ,'chinese' => 'Chinese'
        ,'french' => 'French'
        ,'german' => 'German'
        ,'italian' => 'Italian'
        ,'japanese' => 'Japanese'
        ,'mexican' => 'Mexican'
        ,'spanish' => 'Spanish'
        ,'fusion' => 'Fusion'
      	)
      ,'attributes' => array(
      	'multiple' => 'multiple' // This changes a select field into a multi-select field
      	)
));

piklist( 'field', array(
      'type' => 'select'
      ,'field' => 'gw-course'
      ,'scope' => 'taxonomy'
      ,'label' => 'Choose Course'
      ,'columns' => 4
      ,'choices' => array(
        'entree' => 'Entree'
        ,'side' => 'Side'
        ,'salad' => 'Salad'
        ,'appetizer' => 'Appetizer'
        ,'breakfast' => 'Breakfast'
        ,'lunch' => 'Lunch'
        ,'supper' => 'Supper'
        ,'snack' => 'Snack'
        ,'dessert' => 'Dessert'
      	)
    	,'attributes' => array(
      		'multiple' => 'multiple' // This changes a select field into a multi-select field
      		)
));

piklist( 'field', array(
    	'type' => 'text'
    	,'field' => 'serves'
    	,'label' => __('Serves', 'gw-recipe')
    	,'columns' => 4
    	,'help' => __('Number of servings in the recipe', 'gw-recipe')
    	,'attributes' => array(
      		'class' => 'regular-text'
    		)
    	));

piklist( 'field', array(
    'type' => 'group'
    , 'field' => 'ingredients-add-more'
    ,'add_more' => true
    , 'columns' => 12
    ,'fields' => array(
    	array(
    	'type' => 'text'
    	,'field' => 'quantity'
    	,'label' => __('Quantity', 'gw-recipe')
    	,'columns' => 2
    	,'attributes' => array(
      		'class' => 'regular-text'
    		)
  		),
    	array(
    	'type' => 'text'
    	,'field' => 'measure'
    	,'label' => __('Measure', 'gw-recipe')
    	,'columns' => 3
    	,'attributes' => array(
      		'class' => 'regular-text'
    		)
    	),
    	array(
    	'type' => 'text'
    	,'field' => 'ingredient'
    	,'label' => __('Ingredient', 'gw-recipe')
    	,'columns' => 7
    	,'attributes' => array(
      		'class' => 'regular-text'
    		)
  		)
    )
));

piklist( 'field', array(
    'type' => 'group'
    , 'field' => 'instruction-steps'
    ,'add_more' => true
    , 'columns' => 12
    ,'fields' => array(
    	array(
    	'type' => 'text'
    	,'field' => 'instruction_step_num'
    	,'label' => __('Step #', 'gw-recipe')
    	,'columns' => 2
    	,'attributes' => array(
      		'class' => 'regular-text'
    		)
  		),
    	array(
    	'type' => 'textarea',
    	'field' => 'instruction',
    	'label' => 'Instructions',
    	'columns' => 10,
    	'attributes' => array(
      	'rows' => 10,
      	'class' => 'large-text'
    		)
  		)
    )
));

Here’s the definition of the post-type and the taxonomies.

/*
Plugin Name: i824 Recipes
Plugin URI: http://integr824.com/plugin
Description: This adds recipes post types to WordPress
Version: 0.1
Author: Robert Hust
Author URI: http://integr824.com
Plugin Type: Piklist
License: GPL2
*/

 if (!defined('ABSPATH'))
  {
    exit;
  }

add_filter('piklist_taxonomies', 'recipe_cuisine');
function recipe_cuisine($taxonomies){
  $taxonomies[] = array(
    'post_type' => 'gw-recipe'
    ,'name' => 'gw-cuisine'
    ,'show_admin_column' => true
    ,'configuration' => array(
      'hierarchical' => true
      ,'labels' => piklist('taxonomy_labels', 'Cuisines')
      ,'hide_meta_box' => false
      ,'show_ui' => true
      ,'query_var' => true
      ,'rewrite' => array(
        'slug' => 'gw-cuisine'
      )
    )
  );
  return $taxonomies;
}

add_filter('piklist_taxonomies', 'recipe_course');
function recipe_course($taxonomies){
  $taxonomies[] = array(
    'post_type' => 'gw-recipe'
    ,'name' => 'gw-course'
    ,'show_admin_column' => true
    ,'configuration' => array(
      'hierarchical' => true
      ,'labels' => piklist('taxonomy_labels', 'Courses')
      ,'hide_meta_box' => false
      ,'show_ui' => true
      ,'query_var' => true
      ,'rewrite' => array(
        'slug' => 'gw-course'
      )
    )
  );
  return $taxonomies;
}

add_filter('piklist_taxonomies', 'recipe_tools');
function recipe_tools($taxonomies){
  $taxonomies[] = array(
    'post_type' => 'gw-recipe'
    ,'name' => 'gw-tools'
    ,'show_admin_column' => true
    ,'configuration' => array(
      'hierarchical' => false
      ,'labels' => piklist('taxonomy_labels', 'Tools')
      ,'hide_meta_box' => false
      ,'show_ui' => true
      ,'query_var' => true
      ,'rewrite' => array(
        'slug' => 'gw-course'
      )
    )
  );
  return $taxonomies;
}

add_filter('piklist_post_types', 'recipe_post_types');
  function recipe_post_types($post_types)
  {
    $post_types['gw-recipe'] = array(
      'labels' => piklist('post_type_labels', 'Recipe')
      ,'title' => __('Enter Recipe Name')
      ,'menu_icon' => piklist('url', 'piklist') . '/parts/img/piklist-menu-icon.svg'
      ,'page_icon' => piklist('url', 'piklist') . '/parts/img/piklist-page-icon-32.png'
      ,'supports' => array(
        'title'
        ,'editor'
        ,'excerpt'
        ,'comments'
      )
      ,'public' => true
      ,'admin_body_class' => array(
        'custom-body-class'
      )
      ,'has_archive' => true
      ,'rewrite' => array(
        'slug' => 'gw-recipe'
      )
      ,'capability_type' => 'post'
      ,'edit_columns' => array(
        'title' => __('Recipe')
        ,'author' => __('Assigned to')
      )
    );
    return $post_types;
  }