Start up the game via compiling in Hammer, and add the following to the additional game parameters:
-particles 50000
Ingame, bring the console up and type:
pointfile
Now goto the entity causing the problem (If its a path entity, MAKE SURE IT ISN'T TRIGGERED, or half life will crash when it gets activated. Same forother entities (Which I don't have a list of yet)
Follow the line, it bounces everywhere, and where is appears to go through the wall is where th leak is occouring.
Leaks are very common when you carve in, or with non cubed objects, or when you make a room open up into a cylinder. Also remember that any brushes that are entities don't exist is a sense. Treat it as if they aren't there, and it they connect the inside to the outside (A func_door with no hallway on the otherside), place a bloc bigger than the door in the widdle of it. Same goes for glass.