Your form returns not the elements of the form. But your return part of function is something like:
...
return system_settings_form($form);
}
if we look to this function:
function system_settings_form($form) {
$form['actions']['#type'] = 'actions';
$form['actions']['submit'] = array(
'#type' => 'submit',
'#value' => t('Save configuration'),
);
if (!empty($_POST) && form_get_errors()) {
drupal_set_message(t('The settings have not been saved because of the errors.'), 'error');
}
$form['#submit'][] = 'system_settings_form_submit';
// By default, render the form using theme_system_settings_form().
if (!isset($form['#theme'])) {
$form['#theme'] = 'system_settings_form';
}
return $form;
}
Your problem is: $form['#submit'][] = 'system_settings_form_submit';
this adds another submit function to form. And this function saves variables through variable_set() function:
function system_settings_form_submit($form, &$form_state) {
// Exclude unnecessary elements.
form_state_values_clean($form_state);
foreach ($form_state['values'] as $key => $value) {
if (is_array($value) && isset($form_state['values']['array_filter'])) {
$value = array_keys(array_filter($value));
}
variable_set($key, $value);
}
drupal_set_message(t('The configuration options have been saved.'));
}
So you have to get your settings variables with function variable_get();