If you're doing a bi-directional calibration, and from the left, middle and right sides your #s may differ a bit. How much is the question of the day. From my experience with our printers, its pretty normal to see a difference of 1. If you're getting differences of 3+, the issue is with the platen on your machine. If there is a slight difference, I usually use the # from the middle.
If its greater than 2 then here's some things to check:
Make sure the machine is fully leveled, not only left to right (put the level on the platen), but also front to back. If the machine is "twisted" by the front to back not being level, on each side - that can cause variance.
Both of our machines had the issue of the center being different than the sides. This is due to the platen height ever so slightly varying from side to middle to side. I discovered if I simply "slightly loosened" the screws on either the ends or middle (depending upon direction of # difference) that was usually enough to remedy the difference. If its really bad, and its level and in warranty I'd call Epson.
If not, simply pull your platen off (it seems scary - but its no big deal), and get some thin tape and put it over the mounting brackets of the platen to raise up where needed, and that will provide you a way to "even" out the platen. ...and if you spend enough time (try 1-2 hours), you get all numbers to exactly match.
I've done it, because we regularly run labels with 6 point type -- so its gotta be "tight". --- Hope this helps!