Krakkan

I have had to wait a long long time before it starts clearing and building so i usually go cave exploring for like 15-20 mins when i come back its working. Try removing the quarry block and place it down again, if you use "blue markers" replace them and put down quarry block after. 2 steam engines should be over the top for a regular quarry, i only use a redstone engine but sometimes it takes a long time. For custom quarry dont know if 2 steam engines is enough i would think so it might only take longer time to build. If your using blue markers usually the problem is that you have placed the quarry block first, you need to place it after your done with the "blue torches", atleast from my experience.. Hope something of this helped troubleshooting, also read about the quarry on the wiki might be a good idea, just google that ;)