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Firstly we should point out that you should be applying your dark subtraction before you align and stack any images.
Once you've done that and align and stack your light frames, it's possible that you end up with a dark trail of pixels instead of the red ones you first described. You can treat this a little in Photoshop by copying the layer, apply a slight median blur, and set the layer's blend mode to "lighten only". Might soften the image a little, but all noise reduction techniques will. Try it and see.
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