To me, all your calibration frames looks ok (although, I would recomment taking A LOT of them. Bias specially, is very noisy, and you can see the same patterns in the dark). The flats from the box and the sky flat are very similar (you can judge by yourself by substracting the bias to them, and then divide one by the another with PixelMath, using a expression like this: "$T*mean(flat)/flat" and disable rescaling.
As I said earlier, the problem seems to be with your lights. They have an extra pedestal, that does not match your bias. If there is nothing wrong with the capture settings, or file format, you may also check for parasital light, although for the pedestal value I doubt that this is the problem.
To fix this, as a workaround, open your main bias. Then, create a new ImageContainer, with all the raw light frames in it. Then use PixelMath with the following equation: "$T-mean(bias)", where bias is the identifier of your master frame image. Do not rescale. And apply this instance to the ImageContainer. It should create new files with the bias pedestal substracted. Finally, run the new light through the batchprocessing script, or the image calibration process.