Hi
In the Envisage software there is a setting once you press the CNTRL button, called Line Delay. For the Pro I have found between 2-6 is a good range. For the Pro II - seems best at 2.
I've seen lines at different times and I believe they are also due to other factors
1. Appropriate darks - if you take darks at one temp and the temp changes during an imaging session you can see a range of effects. I take lots of darks at different temps and keep a library of them. Keep the dark temp limit setting below 5 to reduce variation
2. USB 2 - I have had problems with noise and striping using USB 1.1. I stil get problems with USB 2 from time to time if I run other things off USB at the same time. A lot of folk recommend getting a USB 2 hub with separate power source
3. Exposure time - you will see far less stripes and other noise for that matter if you take longer (or many shorter) exposures
Hope this helps
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