Alex, I don't think you should worry about it. The only time you need to worry is if you can't get it fine enough for a good pull... although ideally you should have enough adjustment to choke the machine, it isn't necessary. If it grinds fine enough, you're ok. The nature of the burr set is always going to produce grinds that vary in size slightly, and the amount of runout (unevenness in your burr's surfaces that cause the rubbing on one spot but not another) is probably smaller than that natural variation in size in your grounds, so it probably makes no difference.
That being said, if it REALLY bothers you, here's how you fix that:
Get a height comparator, or a dial gauge set up vertically and build yourself a very sharp indicator pointer on it. You'll have to set up your burr on a round turntable or very even, flat surface and simply rotate by hand. Measure the bottoms of V cuts on the burr to see if there is any variation in height, then to flat surface on top to see if there is any difference as you rotate it. If there is, you cannot change the depth of the V cut; but you CAN change the back face, the flat mounting surface on the bottom. You'll have to mark the highest V cut, mark that point and how much the V cut height differential is, then flip it over and grind that part of the mounting face down by the amount you measured as the height differential.
Would I do it? nope. too much trouble. if you can't live with it, chuck it and get a set of SSP burrs, they are pretty good quality and trued up reasonably well.