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35k ADU sounds quite high for a master flat. What is the well depth of the SX Trius? Have you done a photon transfer curve (PTC) to measure the full well saturation. You'll often find is different from the manufacturer specs. If you read the Onsemi/Trusense specifications the ccd testing is done at 27 and 40 degrees so not representative of the effects of cooling. I understand Sony don't publish any specs hence the reason a PTC is valuable.
The negative value may be due to the fact that the pedestal value is not being considered after the operation. Under adaptive subtraction, have you tried to use pedestal or average bias = 100?
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