Please check that the clocks and bias voltages for the CCDs are clean and correct. You could have a problem with a clock (bad amplitude or timing) or a bias voltage (bad value or noise) that keeps one otherwise good chip from working correctly. Unlike (most) logic chips CCDs, which are mixed analog/digital devices, are not 100% interchangeable. After years of tweaking CCDs from Tektronix, and many other manufacturer's (for telescopes not oscilloscopes) I've found that each one has its own personality.
Good luck.