Not every type of brush will prevent leaks. Your map has to essentially be a container, completely sealed with world geometry. If you've changed any of your world geometry into func_detail brushes, those brushes will not prevent leaks from forming.
It's difficult sometimes to find the leak using the red zig zagging line from the pointfile. There's a technique I use to help me understand and follow the line properly. First, the line will typically start from an entity. I find it's helpful to find where that line starts and then follow it from there. Now, if you're following that line there will be a point (it may even be very very small) where the line will exit the map space. Remember, your map is a container which cannot have even the smallest of holes. You should recognize where the walls of your container are. Where that red line crosses through or between any walls or joints and heads off into the blackness is where your leak is.
If the line crosses straight through a brush the most likely explanation is that the brush is not world geometry. It's probably a func_detail or a displacement or some other entity that will not seal leaks. Your map, your container walls all MUST be made of world geometry.
If the line passes around any brushes or through joints where brushes meet it's most likely there's simply a gap. Even if it's a fraction of a unit, a gap will still cause a leak. Always make sure that your world geometry brushes are right up against one another. It's because of things like this that you should always work with the grid. Also, if 2 corners of your world brushes are touching, that won't necessarily seal the map. Make sure your brushes overlap by at LEAST one unit or more. If they don't you're very likely to have a leak.
Hopefully this helps you out a bit. One of these days somebody ought to write a guide to understanding the pointfile and fixing leaks. If no one else wants to I can probably do that myself late today or tomorrow.
