Well, first thing you should do is make sure you have the latest version of zhlt, which is version 3.4, these are the most efficient tools and will do the best job on your map, if you don't have them, get them
here.
Also, try rotating that brush by 180? to see if that fixes the problem, it might have something to do with world/face texture alignment.
Other than that, I can't think of anything else, you could look
here and see if any of these might help.
Aaron's Stuff