I am speculating that the reason you have more lever travel is because one of the pistons is extended -> thereby requiring displacement of more brake fluid, which perhaps might cause the other piston to retract further - the chambers are connected fluidically, so perhaps if the one piston will not travel back, it is causing the other piston to travel back further, as a certain volume of fluid must be displaced from one piston to the other. IF both pistons are free to move, they will each move a smaller, roughly equal distance.
There are, to my knowledge, only (2) intentional holes within the master cylinder reservoirer - both on the bottom of the chamber. The tiny, needle-point sized one is the one that most often gets gummed up and serves as the fluid return circuit. But, if that were plugged on your bike I'd expect that both pistons wouldn't be retracting properly. But, it bears looking into, I think.