You should try a different company for the repairs if you haven't already. Before you have it done again, check all over the roof with a level and see where the water would run and pool. Also check seams of roofing tar paper. Also, some roofers will just walk around with a pot of tar and dribble it on spots that look suspicious. Using a level to track the path of water should help find the low spots that can be buttressed from beneath to level it out. You might also look into having a drainage system for the roof set up. Check for moisture leaks in the attic too if you have one.
This might be because it is being repaired the wrong way or the wrong place is being repaired. The leak in the top layer, which you will be able to see up on the roof, will probably not be directly above where the leak appears in the roof below. Go to http://www.ehow.com/how_17549_repair-flat-roof.html for more information.