Ok John, once again you are dead right. There is something weird going on with the increments displayed in Peaksite when running a PHA scan. Its a bit hard to explain but basically when the scan is initiated the first baseline voltage in both PfE debug and Peaksite match perfectly. Following this the voltage displayed in Peaksite will lag behind for two measurements and on the 4th measurement "catch up" with what is displayed in PfE. These "catch up" points correspond to the highs of the spikes in the PHA scan. I made sure I used a long count time of 5 seconds to make sure Peaksite had time to "catch up" but it made no difference. Its hard to explain but hopefully the graphic below makes sense.
So basically if I fit a curve to every 3rd point I would have my nice PHA scan....
I did the same with a Gain scan with similar results:
However this was slightly different in that 90% of the time it was only lagging one measurement behind not two like in the PHA scan. There were ocassions when it was 2 measurements behind but not often. So the plateau bumps are still there which i think is another issue, but some of the small "noise" definitely correlates to when it was lagging and when it "caught up"
I then did the same with a bias scan:
And same as the Gain scan, it was lagging every second measurement however there was no obvious effect I could see in the Bias scan?
So I think I am having two separate problems here probably. Weird call lagging from Peaksite for steps in PHA, and a separate problem with Gain electronics for my bumps in my gain scan.
Cheers