Are the distances of the leads all the same? Do you have a 4-Wire IR tester? Check the connections between the chips to be sure that that's not contributing. Using a MUX could certainly introduce the variance. I haven't used them much. You could short each mux pin and apply the same voltage to determine how each input responds and check it's linearity.
Distances are not all equal.
Voltages across the sense resistors are the same. So it is a loss across the pcb traces.
Which I was hoping was not going to happen as it should be a no load path back to the adc. EE fail

Maybe I need to add a resistor to make sure it is a no load path?
I do have a 4wire tester but do not want to scrape the solder mask to enable testing at this stage.
I checked mux input and output and it seems to not affect the signal.
I will do further testing across the range and see if this offset is linear.
If it is we can adjust for it in software.
I would like to migrate to using a ESP8266 for the controller.
Testing is ongoing, getting close to going live.
First run will be a charge only so the cells can rest.
Give us time to tune the discharge programming
I think I have caught 90% of the hardware bugs.
Found myself with the need to discharge/capacity test a lot of cells. Definitely interested in this, and wondering about costs/availability.
Cost.
Depends on your choice of cell holders and power supply.
Let's assume if you are going this route you want as many slots as you can.
JLCPCB has a minimum 5 board order, giving you 80 slots.
Note not all of the ordered PCB need to be populated so you can save a few dollars by having only 4 boards with components on them.
But the major cost is setup and shipping so not really worth it to not populate all boards.
Costing below for least labour intensive smd holder option.
us$
18 Controller. Arduino Mega as code is not currently not optimised.
189 5x populated boards (153 order + 36 shipping)
40 80 x single smd holders
40 80 x tp5100
30 160 x 5w resistors. Use two to keep them below 50% of their rating. Less accidental burn risk.
----
317
Allow for a 400w (12v 34A) power supply. 5w * 80.
A few hours to put everything together.
.Solder on cell holders
.wire board data interlinks.
.wire board power interlinks
For comparison a MCC currently goes for us$180 + shipping.
www.deepcyclepower.com
Availability
The hardware is open source. Current posted revision has some bugs.
Can order your own set from JLCPCB.
My software will be open source too. Although someone else might write a better closed source software for it.