I wouldn't just discount Eagle Point due to there being a difference between your's and somebody else's numbers.
Assuming you had good topo prior to project start (and your site is measured in acres and not square miles), it wouldn't be much of an exercise to figure out what the "correct" number is. You could at least get in the ball park.
To answer your original question, theoretically, all the "earthwork" software should give you the same number. That is, it's just calculating volumes. However, like any computer program, the data it spits out will never be better than the data that's put in. Two major points of interest are the shrink/swell percentages and the amount of topo coverage you have for the existing and finished grades.
I use Land Desktop, but have not really used anything else other than spreadsheet and average-end area. I'd recommend using whatever program you're using to do the design.