Different conditions I'm sure, but maybe you'll find something applicable in my wet trip story...
About a month ago in the Otter Creek Wilderness, WV on the last night of a 2-night trip we got hit with an outer band of hurricane Irene right around 11 pm. We were sheltered from most of the wind by being on the leeward side of the mountain, but the rain was like being in the shower, and was blowing in random directions. Having only a rain jacket but still wanting to hang out with the rest of the group in the rain around the drowned campfire remnants (yes, I am crazy), my pants got soaked. I put them in the vestibule of my single wall tent, along with the rest of my gear. Humidity was 100% when I went to bed (visible fog and mist). It rained off and on all night. Condensation quickly formed, and started dripping on my down bag (Montbell, very new, thus good factory DWR). It was only in the 50's (F), but I didn't see anyplace where my bag had lost loft or the down seemed wet in the morning. I shook the droplets of water off and packed it away. Everything else in the tent was at least as wet as when I had went to bed.
I agree with the others who guess it was mostly the bivy at fault. Your quilt might need a good DWR re-treatment, but I think you'll have to determine that separately.
How much of a gap was there between your shelter and the ground? Maybe a little more ventilation would've helped?