Ajax upload in Ctools Modal Window
I faced the same problem, and I managed to solve it using merlinofchaos's suggestion. I used form_load_include() just after form_state initialization:

  $form_state = array(
    'title' =&gt; t('Add new deal'),
    'ajax' =&gt; TRUE,
    'node' =&gt; $node,
  );

  $form_state['build_info']['args'] = isset($form_state['build_info']['args']) ? $form_state['build_info']['args'] : array($node);
  form_load_include($form_state, 'inc', 'node', 'node.pages');