Sorry, if it's none of my business but...
I've checked your site and looked at the stats of your map, CTF-010011. Those nodecounts are pretty bad (Poly/Node Ratio: 2.44:1 -> Good below 2.15:1) compared to the number of brushes you have and the stage of the development.
Try using semi-solids and make your geometry more precise by limiting off-grid construction...
I have my CTF-Abyss nearly completed (botpathing now) and my stats are:
Brushes: 1501
Zones: 15
Polys: 15794
Nodes: 25384
Poly/Node Ratio: 1.61:1 (Woohoo!!)
My BSP tree is rather unbalanced that's why I'm getting those cool nodecounts (I had a week with killing BSP holes so I earned it) so the slowdowns are caused by places where the visible polys are in a very deep area of the BSP tree...