The following is the alias function reworked to introduce another argument protect_identified. This will prevent aliased sub-queries being escaped twice:

	/**
	 * Specifies an alias for this subquery.
	 *
	 * Note: This only applies if this object is a subquery
	 *
	 * @access public
	 * @param string The alias
	 * @param bool		If to protect identifiers
	 *
	 * @return $this
	 */
	function &alias($alias, $protect_identifiers = true)
	{
		if($this->q_as !== false)
			$this->q_as = ($protect_identifiers ? $this->_protect_identifiers($alias) : $alias);

		return $this;
	}

Cheers,
Stan