video opens in shadowbox AND new link

I suppose youtub.com is a typographic error.

Can you provide a link to see the problem?

Your problem comes from a javascript code that force external links to be opened in a new tab.

I'm not sure if it is exactly External New Tab

If it can be configured to exclude some links, you should exclude youtube links.

Yes confirmed it is that one and it does not have a way to exclude links, only to exclude paths. The feature you would need is to exclude links not paths, so in the path were your youtube links reside, the rest of external links are opened in new tabs if that is what you want.

Your solution is to disable that module or hack it. For example you can hack its external.js file from:

// $Id: external.js,v 1.8 2010/03/22 19:12:55 mcrittenden Exp $
Drupal.behaviors.external = function(context) {
  // Open external links in new tabs.
  $("a[href^=http://]", context).each(function() {
    if(this.href.toLowerCase().indexOf(location.hostname) == -1) {
      $(this).click(externalNewWindow);
    }
  });
  // If the setting is enabled, open PDFs in new tabs.
  if (Drupal.settings.externalpdf) {
    $("a[href*=.pdf]", context).each(function() {
        $(this).click(externalNewWindow);
    });
  };
  // Open any links with class="newtab" in new tabs
  $("a.newtab", context).click(externalNewWindow);

  // Utility function that does the work.
  function externalNewWindow() {
    window.open(this.href);
    return false;
  }
}

to:

// $Id: external.js,v 1.8 2010/03/22 19:12:55 mcrittenden Exp $
Drupal.behaviors.external = function(context) {
  // Open external links in new tabs.
  $("a[href^=http://]", context).each(function() {
    var pattern = /^http:\/\/(www\.)?youtube.com\/.*$/;
    if (pattern.test(this.href.toLowerCase())) return;
    if(this.href.toLowerCase().indexOf(location.hostname) == -1) {
      $(this).click(externalNewWindow);
    }
  });
  // If the setting is enabled, open PDFs in new tabs.
  if (Drupal.settings.externalpdf) {
    $("a[href*=.pdf]", context).each(function() {
        $(this).click(externalNewWindow);
    });
  };
  // Open any links with class="newtab" in new tabs
  $("a.newtab", context).click(externalNewWindow);

  // Utility function that does the work.
  function externalNewWindow() {
    window.open(this.href);
    return false;
  }
}

(I can't highlight this code because php tag does not show the pattern correctly)

But the problem will arise again when you include any other external link you don't want to be opened in a new tab: a vimeo video, an external flash video, ....