Having double capacity shouldn't affect this as we are speaking voltages (in mV) and the device faints when voltage drops too low. And it drops when battery gets empty enough, regardless it's size. For example there is many capacities (in Ah) of batteries for cars, for example 65Ah or 130Ah. Regardless their size their voltage is around 12,8V when full and close to 12 when empty. I am no electrician/engineer so this is basically all my knowledge about elecricity, plus the usual facts: It's blue and hurts

Anyway, for me this kind of situation happened when I still had some battery module loaded, and it makes the device switch itself off because it detects the voltage is dropping too low for the device to operate. So requirement of the calibration is to prevent this happening by unloading the modules. You probably knew this already and I have no solution/ideas what to do. So I guess this was quite an useless post, but I'll publish it anyway..