2 interesting points worth noting: 1) switching from 8bit to 16bit killed the frame rate collection on my laptop even with a 400x400 ROI so I opted to stay with the 8bit avi option. This toggle may have "turned off" the diagonal noise. I cannot prove this but the noise was gone when I started imaging. Earlier in the day, I took various flats and the noise was there. Except for sightly tightening the 2 screws connecting the firewire to the camera (which I have never done, just left it hang) and reoriented the cable not to stress the cheap plastic firewire card that slips into the side of my computer, I did nothing else that would have turned off the noise 2) I also tried to toggle on the FireCapture "derotate", however, again the frame rate was cut by more than half. So my conclusion is to capture 16bit derotated Jupiter raw data, you will need a super fast computer. My company issued Lenovo T400 is 2.4GHz is not scheduled for an upgrade for at least 2 years.
Anyway, I have a ton more data to sift through, but I started my favorite GRS view.