You could try loading the pointfile and tracking it down that way.
This from the help file/
http://collective.valve-erc.com/index.php?go=leaks"Make sure that mapname.pts is being copied into the valvemaps folder along with the compile map (you'll have to move it manually otherwise). The .pts file contains a set of coordinates that form a line of dots that should lead you to the leak. To load the pointfile in the game, bring down the console and type pointfile.
You will see a message similar to 1050 points read, and you should see something similar to the above picture. (You may have to run about your level to find it).
The default engine limit is 2048 points, which may not be enough to trace a line to the leak in your map. If this is the case, start Half-Life at the command prompt with "hl -particles 10000" (or some higher number) to allow the engine to display more particles, and thus trace a longer line to help you find your leak.
When you've loaded the pointfile, type "noclip" to allow you to walk through walls and "r_fullbright 1" to make the map bright so you can see everything. (If you're using Zoner's compile tools, the map will already be fullbright since the RAD process didn't run.) If there are monsters placed in the level, typing 'god' and 'notarget' at the console will make things easier as well. The 'notarget' command causes monsters not to become hostile to your presence, and 'god' makes you immune to damage of any sort. If you noclip outside the level, it might also be useful to type 'gl_clear 1' in the console. This will turn the void into a solid color, rather than the mess that it will be if you're using the glide or opengl renderer.
Once you find the line, follow it. It bounces all over the place, goes in screwy directions, both inside and outside the level. At some point, it will pass through a hole in the walls of your level. There's your leak."
Hope it helps.