WED has serious problems for sure. I once compared WED with Torque Constructor (very similar to Hammer) and realized that all the problems with gaps, rotated blocks, rounding mistakes, texture alignment, csg-subtract a.s.o are WED-only problems. You will not have such problems in Constructor.
You can find the whole story here:
http://www.coniserver.net/ubbthreads/showflat.php/Cat/0/Number/741659/page/0/fpart/all/vc/1Scroll a bit down to my report with the images of the house level that I made to test this tool.
