The silence tell amy when they have her in the chair that she will bring the silence. I think the silence have inpregnated her. Reason I say this is because of two things.
firstly, The silence look to much like the roswell type little green man that is supose to abduct people and pregnant them,
secondly, The reason the tardis can not get a confirmed negative or positive, is because the tardis is a living thing, and we all know that no one can remember the silence, so the tardis is seeing the silence baby in her, but then forgetting it, then redoing the scan and forgetting it and so on, OR we are seeing it from the doctors point of view, he sees a positive but then forgets it and so on.