Lithium batteries are fickle things, they are all created equal but some are more equal than others
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The best way to determine this is with two steps:
Check actual capacity, a lot of RC hobby lithium chargers will have a few features, such as controlled discharge as well as a mah (milli-amp-hour) measurement. discharge the cells (individually) to a set safe minimum voltage (say 3.4v). then fully charge the cells to 4.2v and measure the amount of mah each battery consumed. That will give you an accurate measurement of actual capacity.
Both cells may say they're 3000mah capacity, but one could be 2850 mah, the other could be 3030 mah. A difference as big as that could explain your voltage difference.
The other thing to measure, that would give similar results to what you have got, is each batteries internal resistance. The higher this figure, the less amps you can safely discharge from a cell (as higher internal resistance causes the battery to heat up faster under heavy load, batteries that get too hot break down into lithium gas, puff up and potentially breach their package in a worst case scenario). Having one cell with slightly lower internal resistance than the other also means that cell will be more susceptible to bear more of the load when connected in parallel. Its the "path of least resistance" explanation.
measuring a batteries internal resistance isn't as straight forward as using a multimeter in resistance mode (NEVER DO THIS). Quickest explanation I found for figuring this out is here:
http://www.instructables.com/id/How-to-measure-the-internal-resistance-of-a-batter/
basically, measure the batteries voltage under no load, measure it under a known load, measure the voltage across the load as well as the cell. from that you can compute the batteries internal voltage.
Sorry for the rant, but those are the two best causes of your differential voltages.
A third, much less likely explanation, is that somewhere in your rig, one batteries path to the load and slightly higher resistance than the other path (weak solder joint, poor battery terminal contact, weakened connection wire or different wire lengths from the battery to the load). That you can test with a multimeter (without the batteries installed. Though unlikely, its easy as pie to test.
CJ