I did a quick test with one of our custom boards. Since I have not used your files, these are my settings:
16 bit differential input, (source is buffered with an OP because of the low input resistance of the ADC)
Acquisition time is about 230us (with maximum hardware averaging and long delays)
Reference voltage is 3.3V
For my purposes I record 4 different channels every second.
The following histogram is from 1 channel measured 4 times with 8000 data points each.

So I get better results. even slightly better than your scanB. I also checked that the width of the distribution stays almost the same across the full input voltage range.(increasing a little for higher voltages)
It would be interesting to see how to get the best results, so the more data to compare the more we will know.