Hi Julian,
noise has scale as well as the rest of the image. Typically, noise is small-scale so it appears only in first few layers. Try to make a small preview, taking only background. Then, apply ExtractWaveletLayers script to it. I will create several new images, one for each layer. You'll see lot of noise in layers 1 and 2 and less and less in higher layers. The beauty of using ATWT for noise reduction is, that you can control the amount of noise reduction per layer. Most astronomical images are oversampled (your camera has better resolution than your lens) and there's little information in layer 1 and 2. So, you can apply strong and aggressive noise reduction parameters to these layers and less aggressive noise reduction to higher layers to protect image structures.
regards, Zbynek