allright guys, I'm trying to hang with ya but being a noob it is difficult. This may be a lengthy post and I apologize but I think the more info you have the better you can help me. First of all, this map is based on the place I work, so as far as having things in mind when I started it to reduce certain problems was a bit difficult. Here is some more pics:
In picture one I have clarified where I believe the VIS brush should be. Sorry Storm about the first pic, I wasn't trying to be exact, just give a general idea. Shame on me. Rather than making two VIS brushes, shouldn't I just make one indicated in yellow? This would make AREA 2 not be drawn for anyone above or below the brush area, correct? The problem is anyone standing above the brush in that short hallway should still be able to see part of AREA 2 but the way I have the brush now, I don't think they would.
The second pic is the 3D view of the window to give you a better idea. Sorry about the poor quality, I'm on my system at work.
Below is a pic that gives you a larger view of my map:

The blue lines indicate structural walls.
It is my theory that the real problem lies in AREA 2 because if you look at the bottom of the pic, you see AREA 3 which also has an open window into AREA 2. Now AREA 1 has no LOS with AREA 3 and vice versa, but AREA 2 has LOS with both.
Pantera, to answer your question about the areas of low FPS, I have my spawn point in the middle of AREA 3, you can't see exactly where from my pic, but it's more to your right as you look at your screen. When I pivot towards AREA 1, I see the negative effect of low FPS (around low 30's) and high mtex (around high twenties). As I pivot towards AREA 2, it suffers moreso with FPS going down to the twenties and mtex up to mid thirties. This map has an outside area surrounding the entire inner area as well with glass windows on the north wall of AREA 1 that can see outside.
Some more info on the map, it is extremely large at 1,600,000 visdata. I have everything caulked and my skybox as tight as can be, but I have a lot of prefabs in it. My .map file size is 7.5 megs!! I have no intersecting brushes so everything seems to be fine. I just have it jampacked, I mean it has like 250 static models and I still need to put more in as well as assign my objectives. Once I put the prefabs in initially the .map file size went from about 3 megs to 5.5. I have been doing a fast complile to test it and I'm getting my FPS and mtex from that and I've read that those numbers are never accurate on a fast compile. So basically, maybe my problem is that it is just to jampacked. Comments??