Grill Grates are meant to be used at very high, searing temperatures and for relatively short periods of time -- e.g. for searing steaks, chops and burgers. They don't serve much purpose at lower, slow-cooking temperatures. I use them on my Memphis pellet cooker at 600 and do most cuts in three to six minutes or so depending on thickness and desired doneness. A one-inch steak, for instance, needs only a couple of minutes per side for medium rare. If you are burning meat, you're likely cooking it too long (check the article on steak cookery in my section).
As to uneven cooking, I'd look for something like a disturbed or uneven flame pattern. Remove the GG's and the Weber grids and observe the burners. Webers are known for even heating, usually. I've put the GG's in my Spirit on a couple of occasions to do burgers for the grandkids and never had any significant hot or cold spots. Last thought -- don't remove the Weber grates, use the GG's on top of them as that is the intended method. If you have them right over the bars you may get some uneven patterns.
Good luck. I love my GG's and have never had problems.
Hub