You probably arnt, but just in case, are you taking lights and darks as JPegs?. That wont work, the compression wont allow subtracting jpeg darks from jpeg lights, use RAW only.
Are you using the file calibrate feature?, rather than just combining darks/flats/bias and lights?, just wondering, as you say you are tring "different combinations", and the darks are killing signal, dosent sound right at all.
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