the problem might well be that there is zero dark current and very little sky in your image with such short subs. when you subtract the bias (or the dark) you end up with an image that has lots of negative values where the data in the sub (overlaid with the read noise) was less than the dark/bias. You maybe need to put in a pedestal to protect the data from going negative - PI allows that and I think that a couple of other packages do as well.
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