I think everyone assumed the 2.5 to1 was quarts/pound. Much different than 2.5 liters/kg. Normal mash thickness is about 3L/kg, so you should be just fine at 2.5L. In my early days of batch sparging, I did the double sparge thing, thinking that's what BeerSmith was calling for. I later discovered that draining the mash tun was the first of the 2 steps. I doubt that's causing your low extraction. Stratification of the first and second runnings are common. If you haven't thoroughly mixed after the second runoff, that's likely the problem. You're getting a very dilute sample for your gravity check.