Rolf, Mo, thanks for the feedback. You may not believe this but last night the diagonal noise was completely gone (although some slight vertical noise is now present). You're probably thinking that I've lost my mind but I have attached some new flat data that shows the change. The only new things I tried were:
1) Slighty tightening the 2 screws that hold the firewire to the back of the camera since the heavy cable droops down and will pull out if I step on it by accident.
2) I rerouted the firewire cable to the cheap plastic adapter card that pulls into my laptop and again avoid unecesssary strain from the heavy cable.
3) I tried collecting 16bit fit data only to find that my computer can't seem to keep up with the direct write. (I have not tried .SER but not sure what to do with that format data even if I had it). After finally giving up, I toggled by to 8bit data
4) It was quite cold last night, around 23F which may have helped?
So after "borrowing" the round flourescent light from the basement, my flat light was back in business and I took flats with each channel using the same fps (80/80/45) & histogram (65%) as my actual Jupiter data and no lines to be found. I plan to go out shortly and make some test avis on the sun which is when I first noticed this issue.
In conclusion, it may have been the toggling between 8/16/8bit that turned off the diagonal noise. Point Grey has not seen type of noise before. I will post more data when I get it. It's hard for me to believe that only my Flea3 has this issue. Anyway, keep this trick in mind, it may work for you.