Only unprocessed form_state is stored in drupal_rebuild_form().

It seems drupal_process_form() and drupal_rebuild_form() differ in how they handle the form_state in the form_cache. While the former stores the form_cache from after the form being processed the latter stores it before the form elements are processed. This means data process handlers can’t consistently store data in the $form_state at least in multi-step forms (webform in my case).