template.php not overriding theme.inc

You know, I'm looking at your code above, and I can't see any difference between it and the theme_links() function in theme.inc. What did you change?

What I'm saying is that perhaps it IS working, but it's not having the effect you want. Maybe you should put a big flashing "HEY PAL IT'S WORKING" sign in the code or something, as a debug.

One other possibility: If your template has both phptemplate_links() AND mytheme_links(), I would imagine that the mytheme_links() function would take precedence. This would also be an issue if e.g. you're writing a sub-theme. (That's why Drupal recommends the mytheme_ method.)

EDIT:
Explain what you mean by this:

The strange thing is that if I call it have the same code in both theme.inc and template.php I get an error saying they can't be the same

OK, here's one:

In /modules/wysiwyg/editors/timymce.inc there is this function:

function wysiwyg_tinymce_settings($editor, $config, $theme) {
  $settings = array(
'gecko_spellcheck' => TRUE,
    'button_tile_map' => TRUE, // @todo Add a setting for this.
    'document_base_url' => base_path(),
    'mode' => 'none',
    'plugins' => array(),
    'theme' => $theme,
    'width' => '100%',
    // Strict loading mode must be enabled; otherwise TinyMCE would use
    // document.write() in IE and Chrome.
    'strict_loading_mode' => TRUE,
    // TinyMCE's URL conversion magic breaks Drupal modules that use a special
    // syntax for paths. This makes 'relative_urls' obsolete.
    'convert_urls' => FALSE,
    // The default entity_encoding ('named') converts too many characters in
    // languages (like Greek). Since Drupal supports Unicode, we only convert
    // HTML control characters and invisible characters. TinyMCE always converts
    // XML default characters '&', '<', '>'.
    'entities' => '160,nbsp,173,shy,8194,ensp,8195,emsp,8201,thinsp,8204,zwnj,8205,zwj,8206,lrm,8207,rlm',
  );
  if (isset($config['apply_source_formatting'])) {
    $settings['apply_source_formatting'] = $config['apply_source_formatting'];
  }
  if (isset($config['convert_fonts_to_spans'])) {
    $settings['convert_fonts_to_spans'] = $config['convert_fonts_to_spans'];
  }
  if (isset($config['language'])) {
    $settings['language'] = $config['language'];
  }
  if (isset($config['paste_auto_cleanup_on_paste'])) {
    $settings['paste_auto_cleanup_on_paste'] = $config['paste_auto_cleanup_on_paste'];
  }
  if (isset($config['preformatted'])) {
    $settings['preformatted'] = $config['preformatted'];
  }
  if (isset($config['remove_linebreaks'])) {
    $settings['remove_linebreaks'] = $config['remove_linebreaks'];
  }
  if (isset($config['verify_html'])) {
    $settings['verify_html'] = $config['verify_html'];
  }

  if (!empty($config['css_classes'])) {
    $settings['theme_advanced_styles'] = implode(';', array_filter(explode("\n", str_replace("\r", '', $config['css_classes']))));
  }

  if (isset($config['css_setting'])) {
    if ($config['css_setting'] == 'theme') {
      $settings['content_css'] = implode(',', wysiwyg_get_css());
    }
    else if ($config['css_setting'] == 'self' && isset($config['css_path'])) {
      $settings['content_css'] = strtr($config['css_path'], array('%b' => base_path(), '%t' => path_to_theme()));
    }
  }

You can see I added: 'gecko_spellcheck' => TRUE at the top to turn on firefox spellchecker (which tinymce has off by default). This works BTW.

Aren't I correct in assuming that instead of having to hack the .inc file, I should be able to over-ride the function in template.php and add the spellcheck setting that way?

If not, can you explain why not?
If so, could you give me a clue how I should be doing it?

Thanks for your help.

...that cannot be overriden.

I am trying to overide function theme_cart_review_table($show_subtotal = TRUE) located in ubercart uc_cart_checkout_pane.inc file

So I have copied the function, and renamed it to phptemplate_cart_review_table($show_subtotal = TRUE) in template.php

(i have other overridden functions in there that work)

Made a few changes in the template.php version of the function (nothing major) just added another column into the table it returns

But the changes do not appear on my page and I have cleared the cache many times...even cleared my firefox browser cache hoping it may work...but nothing

Any ideas?