Don't get confused between Pertex and Pertex Shield - they aren't the same. Pertex on its own is highly windproof and extrmely breathable, and water repellent when treated with a hydorphobic chemical (whilst it lasts). It's perfect for general running, but won't keep out prolonged rain or pass kit checks where waterproof is stated. Pertex Shield IS waterproof as it has a polyurethane laminate added to the Pertex face fabric, and will pass a kit check if seams are taped.
This article gives a good summary of its properties:
http://www.backpackinglight.com/cgi-...ex_shield.html