With most lithium-ion packs, the fuel gauge software is adaptive. It needs a training period to get properly calibrated for a given set of cells. During that training period, the battery needs to be fully charged, then discharged to shutdown, a couple of times. Until it gets calibrated, expect odd behaviors, inaccurate capacity indications, etc. Although this chemistry does not suffer from the memory effect that NiCds, eg., are famous for, the digital fuel gauge can introduce artificial capacity reductions that behave much the same way. Running the pack through a full charge/discharge cycle from time to time helps keep the fuel gauge calibrated as the cells age.