I think this is due to the thermal noise adding into the flat image. Please test Flat-Bias and see if there is some change.
Because of the readout , the buttom pixel will wait more time to be readout so the thermal noise is bigger. All interline CCD(includes,
SONY's , and Kodak KAI series) are effect by this thermal noise.
You can also test high download speed and see if the center is moved.