I ran into this same issue when using $base_url in page.tpl.php in the following:

    print l(theme('image', array('path'=>path_to_theme().'/css/images/logo_orig.png')), $base_url, array('html' => 'true'));

I fixed this by preprocessing `$base_url` in template.php:

    function yourTheme_preprocess_page(&$vars, $hook) {
      global $base_url;
      $vars['base_url'] = $base_url;
    }

So, I'm thinking you can preprocess you html template as well. This will be cleaner that calling a global in your tpl directly.