Its a parallax problem. Too much space between your optic and your bore means the optic is "looking down on the target" too much and adjustments at various ranges become a pain in the ass.
Normally with your iron sights you have about four inches of parallax and the adjustments work pretty well. If you mount the EOtech on a flattop receiver it'll cowitness with the irons and you still have about four inches of parallax. The adjustments on the optic are designed for this much parallax because the designers know how tall the optic is.
Now, when you put the optic on top of the carry handle, you have the four inch height of the reticle over the EOtech's bottom, plus about a half inch of picatinny rail that you had to attach to the carry handle so the optic can be mounted. Now you have a total of roughly eight and a half inches of space between the bore and your sight line.
So now, if you sight in the gun at, say, 25 yards, the bore is at a zero degree angle, shooting straight to 25 yards, and the optic is "looking down" at the target at a significant angle so the point of aim and the point of impact will coincide at 25 yards. If you move the target from 25 to 100 yards without adjusting the optic, as you sight through the optic now your zero is still 25 yards, but you've brought the optic "up" so to speak because the target is further away. Your point of impact will be ludicrously, rediculously high by a number of FEET, not inches. In addition, your adjustments are screwed up, you'll find that the 1/4 inch per click that the optic is supposed to have doesn't apply anymore, although the difference is minimal its mathematically there.
If you sight in the gun at 100 yards and go back to shooting at 25 yards, the point of impact will be significantly low. Its basic trig really.
The only solution is to get rid of the extra parallax by utilizing a mount that attaches to your carry handle but mounts the optic back down near the bore. These so-called "gooseneck" mounts are expensive, but do effectively solve the problem. Here's a nice adjustable one designed specifically for the EOtech:
www.midwayusa.com/eproductpage.exe/showproduct?saleitemid=159785Ignore the cheap one made by leapers and marketed by Tapco. Its garbage, I bought one as a gift for a friend and was embarrassed when the mounting screw broke on its first trip out to the range. The mounting screw was made of pot metal and held in place by a small roll pin. Everything popped as soon as it was tightened down.