Creating a custom registration page
I found what was causing the problem with not being able to display form elements as described above. The issue was this line in my templates file:

function mytheme_preprocess_user_register(&amp;$variables) {

   $variables['intro_text'] = t('some text.');
   $variables['rendered'] = drupal_render($variables['form']);
}


It looks as though you can only call drupal_render once. Any subsequent calls to drupal_render are ignored as Drupal as already marked the code as rendered. There should be a way to force a re-render if necessary or be able to get the already rendered results. If someone knows how to do this please reply to this post.

The solution was to remove this line from the templates.php file and everything worked.