Just because you have the mouth of the bivy sack open does not mean you will avoid getting condensation further down inside the bivy sack. The moisture coming off your body will diffuse outwards through the SB or Quilt until it hits something which is below the dew point. And then it will condense. Basic physics.
Whether the surface it condenses on is silnylon, GoreTex or plain fabric does not matter: if it is below the dew point condensation will form. Of course, once you have a film of water there the 'breathability' of a membrane goes to pot. Tough.
In your case it would seem that the bivy sack was the right temperature for condensation to form. So it did.
> Are Gore-Tex bivvy sacks just a bad idea in cold weather?
Actually, the real problem is that the surface of the outer layer (a bivy bag in this case) was too close to your SB. If you had been in a tent you would still have experienced the same condensation, but it would have formed on the inside of the tent, well away from your SB. And your SB would probably have stayed fairly dry.
Now, one might object to this for two reasons.
* 'But I want to use a bivy bag, not a tent.' No problem, carry on. You will just get a wet SB.
* 'What if there is wind: it will shake the condensation down on me.' Actually, it is more likely that the wind will blow the moisture out of the tent, keeping the inside of the tent dry. I have experienced that many times in the snow.