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.