My understanding of php objects isn't deep enough to know why this problem is occurring, but I've found the trouble spot and some symptoms. Maybe someone else can take it farther. The pinch occurs at CKFinder_Connector_CommandHandler_CommandHandlerBase::checkConnector. The unaltered function is:

    protected function checkConnector()
    {
        $_config =& CKFinder_Connector_Core_Factory::getInstance("Core_Config");
        if (!$_config->getIsEnabled()) {
            $this->_errorHandler->throwError(CKFINDER_CONNECTOR_ERROR_CONNECTOR_DISABLED);
        }
    }
 

I added some code to dump values to a file to try to see why the if{} was firing:

    protected function checkConnector()
    {
        $_config =& CKFinder_Connector_Core_Factory::getInstance("Core_Config");
/* !Debug code begins here */
          $debug_isEnabled = print_r($_config->getIsEnabled());
          $f = fopen("/Users/shawn/debug.txt", "a"); 
          fwrite($f, "\n" . '$_config->getIsEnabled() returns ' . $debug_isEnabled . ' in checkConnector() through print_r');
          fwrite($f, "\n" . '$_config->getIsEnabled() returns ' . $_config->getIsEnabled() . ' in checkConnector() as a method call'); 
          fclose($f);
 /* debug code ends. */

        if (!$_config->getIsEnabled()) {
 /* !Debug code begins here */
          $f = fopen("/Users/shawn/debug.txt", "a"); 
          fwrite($f, "\n" . 'if(!$_config->getIsEnabled()) still fires in checkConnector()'); 
          fclose($f);
 /* debug code ends. */

            $this->_errorHandler->throwError(CKFINDER_CONNECTOR_ERROR_CONNECTOR_DISABLED);
        }
    }
 

When 'allow CKFinder file uploads' is set only for authenticated user, the values dump as follows:

$_config->getIsEnabled() returns 1 in checkConnector() through print_r
$_config->getIsEnabled() returns in checkConnector() as a method call
if(!$_config->getIsEnabled()) still fires in checkConnector()

So $_config->getIsEnabled() appears empty when accessed directly.

When 'allow CKFinder file uploads' is set only for anonymous and authenticated users, the values dump as follows:

$_config->getIsEnabled() returns 1 in checkConnector() through print_r
$_config->getIsEnabled() returns 1 in checkConnector() as a method call

So why doesn't the method call return properly when only the authenticated user is granted perm? Is there a type problem of some kind here?

Sometimes it's the simple things - mistake in the text of the cookie domain in <drupal base>/sites/default/settings.php

Cookie setting doesn't matter if you don't have to be authenticated.