There are a couple of possible culprits, the most probable one being that if you picked the numbers out of a chart, the different calculators may use different ERD values. Some use the value where the nipple meets the rim - which would leave your spokes a tad short, others add a few mm to get full penetration of the spoke into the nipple.
Some take spoke stretch into account if you enter a thin spoke etc.
The recommended way is to buy the rim, and measure the rim to where YOU want the spokes to end up, and use that number. You really shouldn't be seeing 3 mm difference for the same calculations using the same input.