K.,
My husband and I went through this exact same thing with our fourth child. Started out with a routine ultrasound at 11 weeks. The nucual fold was "thick". So we went for the level II ultasound which confirmed the fold was abnormally thick. From there we had the blood screenings and met with a genetic counselor. It seemed like every test we had our odds of our baby having down syndrome was a bit higher. We had ultrasounds every few weeks to check for "soft" markers. Which can include heart, nasal, and stomach malformations. All of these came back fine, but we were monitored very closely. After many many prayers, we chose not to have the amnio. We decided that for us the risk to the pregnancy didn't outway the benefit of knowing.
Long story short. Today we have a fantastic and healthy 18 month old. And after we started to discuss this with friends and family there was a surprisingly high number of people who had experienced the same thing. This is just an opinion, but I think that this testing is relatively "new" and still has some "tweaking" to be done. My thought on this is based on the fact that of the 5 people I know that have gone through this all of our babies have been fine.
I am not trying to give you rose colored lens, please listen to your doctor and do what is right for you and your family.
We used the approach of expect the worst pray for the best...I know this is the scariest thing in the world and my heart goes out to you. Try to focus on the positive and not let this get you too crazy.
You are more than welcome to contact me at ____@____.com
Good luck!