Compile and run your map then bring down the console using the ~ key.
Type pointfile and you should see a series of white dots running thru your level. They will travel in all kinds of crazy directions, just follow them til they run thru the wall, that's where your leak is. Then go back to hammer, zoom in to grid setting 1, you should be able to see the leak.
If the dots don't show up, add -particles 999999 to your command line. By that I mean, when you hit the compile button (F9) you will get window for compiling, look at the top and you will see the commands such as hl.exe -deathmatch 1 and so on. Add the particle statement to the end of that. Then run, type pointfile again.
Hope it helps. Key is to make sure you don't have subpixel vertices in your map, which can happen.