Could you post screenshots of the problem? It may be because the giant box around the level, which leaks into that box (which is huge), is confusing VVIS.

My first suggestion is to raise the grid size (with the "]" button, "[" lowers it) and seal off the interior, then get rid of the 104809x1860x3583 unit box around it. A box around your level is a bad way to fix leaks, because VIS then has to compile everything outside your level. You also have a lot of intersecting brushes, which make the compile take longer and hurt the maps performance.

Someone here can help you, but I think this is a topic for the HL2 editing forums.