Are there things outside of the skybox?
Are the brushes any kind of entity? Are you compiling with all point entities off? There is a third thing here that I was going to ask and forgot.
If you're compiling with zero entities except areaportals, it always leaks for no reason. Compile with at least some point entities in the map.
If I'm reading your post right.
When you fix an error by yourself, post the solution