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I have had some trouble in the past with a 694 CCD sensor that showed pattern noise sometimes and other times not. It cleaned up with a good bias. In that case it was the microlenses showing up I think. It wouldn't be that visible unless the image was stretched a fair bit. Regardless of what its an image of its safe to say its fixed pattern noise. It may be the circuitry setout on the sensor or the microlenses. It does not matter as it handles the same way.
Try making a better bias out of a large number of bias frames and see if that helps. Make sure your bias is at the same temp and gain as the lights. You can get odd effects if darks and biases don't match the lights exactly.
Greg
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