ADC error for low-voltage measurements
You will be very lucky if you can use the bottom 50 mV of an ADC as a calibration point. I usually avoid the bottom and top 50 mV of the quoted range because of gain slope and zero offset problems. 

It does indeed look like you are calibrating with 0 volts fed into the input but you will probably get the same "zero" digital output value with maybe +20 mV fed into the input.

I would calibrate at just below maximum and just above minimum to ensure lowest error for the major part of the range.