Signal tap II list files

I have a rogowski coil rated for a high current device so I'm only getting about 10% of the range of my adc which is giving me a very small waveform to look at in the line chart. I could recompile throwing in some logic to convert the 12 bit number to a 8 bit number to make the line chart more readable but if it displays the same problem or not I still don't understand how the waveform is shifted across the vertical axis when I graph the data in the list file.

The problem I have is that in the oscilloscope there is clear noise on these certain areas of the waveform and very nice in the other. Large enough that there is no way you would get a nice waveform. You would see the values oscillate by a decent amount in this area of the waveform. Now with the values that signal tap gives me, it shows these areas reversed. I don't see how this is happening other then a vertical axis shifting.