Well, it would probably help to get screenshots of the BAD areas. Looking at a good area is hard to give pointers on fixing the bad areas.
Make sure you DIDN'T func_static your walls, just trims.
Visportals (when you use console to show them) basically draw out areas in the airspace of your mission. They get split by 2 things.
1: brushes. So if you have a flat wall with a wood beam running up it's middle you will get 3 vis_leafs. One across the room where the pillar is and one on each side.
basically your one room has been split into 3 parts.
If you make that beam a func_static it will be one. You will see blue lines around each airspace (visleaf). Fewer is better.
2:grid lines. The red lines on the grid every 1024(?) make vis_leafs no matter what.
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So first you need to make sure you don't have just a few huge vis_leafs (making all walls func_static would do this).
You need the walls to block views into other areas. Lots of corners helps.