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The dark frame optimization process depends on the data you are calibrating (it attempts to optimize SNR in the calibrated frames by adjusting the scaling of the dark master) so you can get different results with different data sets.
You haven't done something like subtracting the bias from the master dark twice, have you? If you calibrated the darks with bias subtraction when you created the master dark and then calibrated the lights with the box to calibrate the master dark ticked then that would happen...
Otherwise, if you can upload the master files and a few lights somewhere I'd be happy to take a look at them.
Cheers,
Rick.
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