In all of my custom post types I can no longer change or select a taxonomy. It shows me what was selected before the upgrade, but I can no longer modify the seletions. When I click save, it says saved correctly, but it never actually saves the new selection. In one I have check box as the option, and the other is a select field.

Did the scope method change in the upgrade?

Example:

piklist('field', array(
    'type' => 'checkbox'
    ,'scope' => 'taxonomy'
    ,'field' => 'trip-type'
    ,'label' => 'Trip Type'
    ,'choices' => piklist(
      get_terms('trip-type', array(
        'hide_empty' => false
      ))
      ,array(
        'term_id'
        ,'name'
      )
    )
  ));

Here is my created Taxonomy from my main plugin file:

$taxonomies[] = array(
      'post_type' => 'post_mission_trip'
      ,'name' => 'trip-type'
      ,'show_admin_column' => true
      ,'hide_meta_box' => false
      ,'configuration' => array(
        'hierarchical' => false
        ,'labels' => piklist('taxonomy_labels', 'Trip Type')
        ,'show_ui' => true
        ,'query_var' => true
        ,'rewrite' => array( 
          'slug' => 'trip-type' 
        )
      )
    );