If you are facing a problem like in magento admin you can’t save acl information for api / admin user, here is the solution :-

For Api User overwrite the constructor of the block Mage_Adminhtml_Block_Api_Tab_Rolesedit with following function :-

 public function __construct() {
        Mage_Adminhtml_Block_Widget_Form :: __construct();

        $rid = Mage::app()->getRequest()->getParam('rid', false);

        $resources = Mage::getModel('api/roles')->getResourcesList();

        $rules_set = Mage::getResourceModel('api/rules_collection')->getByRoles($rid)->load();

        $selrids = array();
        foreach ($rules_set->getItems() as $item) {
            //changed the code here..
            if (array_key_exists($item->getResource_id(), $resources) && $item->getPermission() == 'allow') {
                $resources[$item->getResource_id()]['checked'] = true;
                array_push($selrids, $item->getResource_id());