The cells have some internal resistance as well, usually on the order of 0.2 Ohms or so.  Sometimes a lot higher.

The higher it is, the more the cell wastes power and heats up during charging and discharging.

I went looking and I believe I can measure the internal cell resistance with my current rig, but it will require some code changes.  It basically involves shutting off the load resistor, measuring the voltage, turning it on 100%, measuring the voltage drop inline with my known resistor, and then calculating the missing resistance.  You have to do this quickly so you can negate the cell discharging during the measurement.

The code currently doesn't handle intermittent discharging as it relies on a constant rate being kept from one cycle to the next and so this would throw off the numbers.  

On the todo list.