It seems that PHP does not support setting of properties with arguments. This is how I got around the problem:
// Object with method I want to set
$auth = new COM("AUTHXOCX.AuthXOCXCtrl.1");
// ScriptControl
$oScript = new COM("MSScriptControl.ScriptControl");
$oScript->Language = "VBScript";
$oScript->AllowUI = TRUE;
// Add out object to the control
$oScript->AddObject('auth', $auth, true);
// Create a VBScript function that allow me to set them
$oScript->AddCode(
'Function fixAccess(accessname)
auth.AuthDataReferrerEnabled(accessname) = 1
auth.AuthDataAuthentiXDBEnabled(accessname) = 0
End Function');
// Execute function
$oScript->Run("fixAccess", $dir);