How do I save the values for a custom fieldset?
One way to do it would be in hook_form_alter add a custom validate handler:

$form['#validate'][] = 'my_custom_validate_handler';


then you should be able to do (double check that with debug(), print_r() or devel): 

function my_custom_validate_handler(&amp;$form, &amp;$form_state) {

    $form_state['values']['group_access']['und'][0]['value'] = 1;

}


Another way would be to set a '#default_value' and it should be something like that:

$form['group_access']['und'][0]['default']['#default_value'] = 1


Hope that helps!