node-story.tpl.php Not Being Used

Thank you for your kind responses.

Firstly, I am not doing too much on the preprocess side in template.php. Here is the file just in case you see something that might be causing this:

<?php
// $Id: template.php,v 1.13 2008/05/13 09:19:13 johnalbin Exp $

/**
 * @file
 *
 * OVERRIDING THEME FUNCTIONS
 *
 * The Drupal theme system uses special theme functions to generate HTML output
 * automatically. Often we wish to customize this HTML output. To do this, we
 * have to override the theme function. You have to first find the theme
 * function that generates the output, and then "catch" it and modify it here.
 * The easiest way to do it is to copy the original function in its entirety and
 * paste it here, changing the prefix from theme_ to agape_. For example:
 *
 *   original: theme_breadcrumb()
 *   theme override: agape_breadcrumb()
 *
 * where agape is the name of your sub-theme. For example, the zen_classic
 * theme would define a zen_classic_breadcrumb() function.
 *
 * If you would like to override any of the theme functions used in Zen core,
 * you should first look at how Zen core implements those functions:
 *   theme_breadcrumbs()      in zen/template.php
 *   theme_menu_item_link()   in zen/template-menus.php
 *   theme_menu_local_tasks() in zen/template-menus.php
 */


/*
 * Add any conditional stylesheets you will need for this sub-theme.
 *
 * To add stylesheets that ALWAYS need to be included, you should add them to
 * your .info file instead. Only use this section if you are including
 * stylesheets based on certain conditions.
 */


drupal_add_js(path_to_theme() . '/jquery.protify-0.2.js', 'theme', 'header');
drupal_add_js(path_to_theme() . '/agape.js', 'theme', 'header');


//$menu_item = menu_get_item();
//$menu_link = menu_link_load(db_result(db_query("SELECT mlid FROM {menu_links} WHERE link_path = '%s'", $menu_item['href'])));
//$use_menu = $menu_link['menu_name'];
//menu_set_active_menu_name($use_menu);

/**
 * Implementation of HOOK_theme().
 */
function agape_theme(&$existing, $type, $theme, $path) {
  return zen_theme($existing, $type, $theme, $path);
}

function active_first_level_menu_item() {
	$trail_head = "";
	$level = 1;
	$tree = menu_tree_page_data(variable_get('menu_primary_links_source', 'primary-links'));
	while ($level-- > 0 && $tree) {
    // Loop through the current level's items until we find one that is in trail.
    while ($item = array_shift($tree)) {
      if ($item['link']['in_active_trail']) {
        // If the item is in the active trail, we continue in the subtree.
				$trail_head = $item['link']['title'];
        break;
      }
    }
  }
	return $trail_head;
}

/**
 * Override or insert PHPTemplate variables into the page templates.
 *
 * @param $vars
 *   A sequential array of variables to pass to the theme template.
 * @param $hook
 *   The name of the theme function being called ("page" in this case.)
 */
function agape_preprocess_page(&$vars, $hook) {
  $vars['sample_variable'] = t('Lorem ipsum.');
 	$vars['active'] = active_first_level_menu_item();
	
}

/**
* Use a slash instead of an '>' in breadcrumbs 
*/

function agape_breadcrumb($breadcrumb) {
  if (!empty($breadcrumb)) {
    return '<div class="breadcrumb">'. implode(' / ', $breadcrumb) .'</div>';
  }
}

function agape_preprocess_content_field(&$variables) {  
  // Some customisations for story content type
  // Turn off some field labels for story
  if ($variables['node']->type == 'story' && in_array($variables['field_name'], array('field_subtitle', 'field_source', 'field_date'))) {
    $variables['label_display'] = 'hidden';
  }

  // CCK field items default to using <div>
  $variables['field_list_start_tag'] = '';
  $variables['field_list_end_tag'] = '';
  $variables['field_list_item_tag'] = 'div';

  // For some cases, change this to <ul> and <li>
  if (($variables['field_name'] == 'field_headlines' && $variables['teaser']) ||
      ($variables['field_name'] == 'field_stories')) {
    $variables['field_list_start_tag'] = '<ul>';
    $variables['field_list_end_tag'] = '</ul>';
    $variables['field_list_item_tag'] = 'li';
  }
}

/**
 * Override or insert PHPTemplate variables into the node templates.
 *
 * @param $vars
 *   A sequential array of variables to pass to the theme template.
 * @param $hook
 *   The name of the theme function being called ("node" in this case.)
 */

function agape_preprocess_node(&$variables, $hook) {
  zen_preprocess_node($variables, $hook);
  $node = $variables['node'];

  // Add a node-type-teaser suggestion
  if ($node->teaser) {
    $variables['template_files'][] = 'node-'. $node->type . '-teaser';
  }

  $variables['body_content'] = $node->content['body']['#value'];

  // If there is an extracted teaser image, do some processing
  if (isset($node->teaser_pp_img)) {
    $variables['teaser_pp_img'] = $node->content['teaser_pp_img']['#value'];
  }  
}

/**
 * Override theme_custom_local_tasks to make the css look like zen_menu_local_tasks()
 */
function agape_custom_local_tasks($primary = '', $secondary = '') {
  $output = '';

  if ($primary) {
    $output .= '<ul class="tabs primary clear-block">' . $primary . '</ul>';
  }
  if ($secondary) {
    $output .= '<ul class="tabs secondary clear-block">' . $secondary . '</ul>';
  }

  return $output;
}

Secondly, when I make a change to node.tpl.php in either Zen or the subtheme, nothing happens. It appears to be using the only other node.tpl.php, which is in /modules/views/themes! It's completely ignoring node templates in my subtheme, but it does recognize my standard Views templates (e.g., views-view-field.tpl.php, etc.) in the subtheme. Just not node templates...

How odd... I don't know how to troubleshoot this.

Thanks for your response. It is an actual story content type... I am using the right name. As I said, even the Devel module recognizes "node-story.tpl.php" as a candidate for this exact content type output.

As for the template suggestion, I placed it in Zen in the hope that it would work, but it didn't help, so my suggestions are now only in the subtheme.