check for correct grain absorption rates, check the include dead space in calc box and make sure it is correct for your setup. Post boil, check that the numbers it's using accurately reflect your experiences with boil-off rate and loss to trub.
BS can get pretty close, but only if you enter accurate numbers based on your actual setup and experiences.
If it's something that you haven't had happen before...maybe it was a simple measurement error with water additions?
It does sound like the total water you used is too low, at about 7G, you would lose some to the grain, dead space, and trub, with 7G in the mash, i'd expect to get 5.5G +- a quart into the boil pot. which would give you about 4G into the fermenter.