As a workaround there can be added the following OnClientShow handler to the RadWindowManager Client Show event.
function OnClientShow(sender, args) {
	var container = sender.get_contentElement();
	var formDecorator = $find("radCheckBoxDecorator");
	$telerik.$('.rfdRealInput', container).removeClass('rfdRealInput');
	formDecorator.decorate(container);
}