Peter,
as far as I know, Windstopper has no PU layer.
Take a look at following article:
http://www.outdoorsmagic.com/news/article/mps/UAN/3921/V/2/SP/
Somewhere in the middle of the page you'll find a part about Windstopper passing a bubbler test (meaning air passes through it). This should be proof enough that Windstopper has no Pu layer.
About Windstopper being less breathable than gore-tex, I don't know how reliable Patagonia's method is. But I've seen all sorts of figures based on the RET ratings Gore preferes. Some claim RET values are lower than 4, other sources claim values between 6 and 3 (which are comparable values as classic gore-tex). As a reminder, Gore-tex XCR was claimed to have an RET lower than 6, while the new/updated Pro Shell performs a bit better (on average lower than 5 with some values going as low as 3 and even 2,5). And yes, Pro Shell still has the PU-layer. So strangely enough Pro Shell with PU seems to perform better than Windstopper without PU (or eVENT).
Question is of course how relevant these ratings are for realtime comfort. Studies have shown that air permeability is more important for comfort than breathability = moisture vapor transpiration and both eVENT and Windstopper seem to be slightly air permeable.
Still, why would Pro Shell have better RET values than eVENT or Windstopper? Well, my guess is that this could be explained by the different face fabrics and lining being used. Although I've never used a windstopper garment myself, my impression is that windstopper laminates are quite often thicker and heavier than gore-tex laminates e.g. one manufacturer uses different gore-tex laminates with the heaviest around 4,8 oz/yd² while their windstopper laminates range between 5,2 and 8 oz/yd². That's my guess.
BTW, there's such a wide range available in gore-tex and windstopper laminates that it's actually hard to say what performs better.
