I have a decent computer which in theory should run this game at a constant 60fps, the standard game does actually run at that, but I find in some custom stories I experience a lot of jerky moments were fps drops to below 50 (e.g, Gary Dark Secrets, Followed by Death, and Insanity Nocturnal Confusion).
I have tried lowering SSAO quality to medium and samples to 8, but this doesnt seem to have helped. Is there any way to get CS to run smoothly at 60fps? My system specs:
AMD Phenom II X6 1090T @ 3.8ghz
Zotac GTX 670 AMP! Edition
8GB DDR3 RAM (9 9 9 24)
On my admittedly bad computer, I find that turning down shadow quality often gives a large frame rate boost. In my case it goes from unplayable to barely playable. However in your case it may solve your problem. If push comes to shove, if I remember correctly, you can even turn off shadows as well. I am not quite as sure about that one though.
It can also help in certain sections to turn off world reflection and other features. In general the more features you turn off or lower the better the frame rate. Beware! The game will become uglier though.
To be honest; If the custom story's maps don't look as good as the main campaign's but runs slower, then it's a badly made custom story. Maps need to be designed in such a way that occlusion culling can take effect. And a lot of people are oblivious to this. Other misuses of resources can also lead to laggy maps, like; too many particle and/or light effects, large spaces with too much junk in them, extremely scaled down textures (that result in repeating textures), large bodies of water that reflect the entire map etc...
Map builders always need to make sure that gaps in walls are completely closed up, they need to make sure that they use plenty of turning corridors...you get the picture. Your PC is definitely not slow. Mine is a Core2Duo e8200 with a geforce 8800gt. And although i don't use AntiAliasing, I do not compromise the graphics (I keep shadows on, world reflections on etc...) and Amnesia's main campaign ran at a constant of 60fps. So...yea, it's not your PC's fault.
Like Dash said, it's probably just poor design in the custom stories.