Li-Ion batteries don’t need any burning in but one stored for a very,
very long time (years) can build up an internal layer of reaction by-products that can affect performance. Cycling the battery can help get rid of some of that layer.
Though that much of a difference in internal resistance indicates to me that other factors, external to the battery, could have been involved. These chargers are very sensitive to contact pressure and internal resistance can vary wildly depending on battery temperature and state-of-charge. A fully charged battery just slightly warm internally can have a much lower IR than one that is less than fully charged and cool.
Comparing two batteries requires that both be charged the same way, in the same charger slot, and allowed to rest the same amount of time before testing. Then, remove the batteries, discharge them, and repeat the test to see if there are any inconsistencies in the measurements. Then, swap slots and repeat the tests twice again. It’s not needed to do this every time once you have confirmed that the results are consistent but it should be done at least once before putting too much trust in our results. There are just too many variables otherwise that can affect the readings.
And, yes, it’s as boring to do as it sounds.
There’s probably no way for us to really know what’s going on though without buying several more mods with those batteries and testing them.