Air flow could also have something to do with it, especially with auto (wind activated) batts. Aside form all the various liquid and equipment properties which affect it, perfect vapor is a proper balance of heat, moisture, and air flow, the right mixture results in the ideal outcome just about the way a car's intake manifold and combustion chamber works. Fine tuning a carburetor can improve performance just like tweaking an atty can. If any physical difference in the connections between atty and batt apply more precise air flow to the 'perfect vapor equation', this can make one batt perform better than another. I had an XL Evo batt that did not work as well as a standard one for this reason, having a wind operated switch really complicated things further and resulted in inconsistency from batt to batt.
Larger batts can also make a difference, particularly when they can better handle the amperage pulled from a 510 atty. I think Scot EE's explanation of the power drain curve plays a big roll here. 10440's are a good example of Li-Ion batts that can have deplorably fast but drawn out drop in power and result in some slow suffering.