I would watch a charge and see what is happening with the current as time goes on. Your charger should be able to charge a 2s pack at 6A with no problems, and as you say it should only take an hour from flat.
Some packs will take a long time to balance, sometimes it can be an issue with the charger, sometimes it can be that the cells inside the pack are well out of balance. But it is unusual for the normal charge to take so long. The chargers will tend drop the current towards the end of the charge to try and prevent overcharging in non-balance mode, watch and see when the current starts to drop.
A charger issue can sometime be overcome by checking the contacts on the leads. I'd be wary of any battery that regularly takes a very long time to balance, it suggests that there is a weak cell in there. 3.2-3.4 is a nice safe cutoff voltage, don't change it, and you will gain very little by doing so, the cell voltage will drop very suddenly towards the end of a run and very little capacity is left to be used.