[Lt. havoc]

There's a simple reason why you can and can't shoot through certain rails.
When map making the brush used to make the rail is textured on 1 side with the rail texture (what you see). The other side can be textured by any number of invisible clips. Certain clips have certain functions (stopping players, adding the effects of grass, metal, wood etc to a particular regions).
Now its the use of the clip type which was applied to the side of the rail and its property which prevent you from shooting through it. It took me quite a while for find the right combination to allow players to shoot through rails in my maps. Unfortunately those properties are built into Remagen and we all have to live with it.