Asimov, thanks I will give that ago I have been using YUY2 - RGB24 so that could be my problems. I just had a try with Y800-Y800 settings in my lounge room, all seemed good but I notice you have to turn on DeBayering to set the histogram levels and then turn it off to record is this correct? I went away from Y800 as a had black and white images and no histogram to adjust, you learn from your mistakes

I also noticed there are 4 force debayer modes is Autostakkert does it matter which I use?
Clayton, thanks for the advice on the AVI, no excursions it was my best ever alignment. I think as Asimov pointed out it looks like it may be the codecs and contrainer choice I had used to attempt to get a histogram, not realising I could turn on and of DeBayering to achieve this so I did not need the RGB24 setting along with YUY2. I have attached an image of my AVI in AS!2 before castrator and as you can see most was an unusable red line and it would not proceed. The second is after castrator so using castrator can help although I lost 50% the AVI when it went into AS!2 it still gave a better result than the 100% of frames stacked throught registax.
Castrator may still be handy if AS!2 wont load the AVI.