In general blinking does mean balancing or excess charge being removed. The cells which have the lowest capacity fill up faster and the balancing keeps these at 4.2 per cell while the others catch up.
Depending on the capacity difference of the cells the amount of balancing power available and the health of the cells it can take from a few minutes to hours for all of the cells to become fully charged and balanced.
Limitimg the flight time(amount discharged) will prevent the inbalance from being as bad and they should charge and balance faster. A chareger which has a LCD display and shows each cell's voltage is a lot beter than flashing LEDs.