@ijed: Could hug both the concave wall on the right and the convex on the left. I as well thought it could be someting other than the stair in question that caused the issue, that's why I tried deleting the step to see if the issue persisted. And nope, as soon as it was gone nothing blocked the player's movement. Again, the error occured even if I remade the step from scratch.
The clip brush is not a slope, here's a picture of how it looks in the editor:
http://img339.imageshack.us/img339/1210/quarkclipping.jpg
With the intersecting brushes, I take it you mean where the curvy white walls meet? They are in fact on grid, both the corners and the intersection.
@negke: So as the amount of detail in maps increases, so may issues like these? If I block out certain details with completely square clip brushes (such as lightning fixtures or computers dug into a wall) throughout the map, would that help eliminate such errors? I was thinking of doing this after I finished up the entire map's brushwork, but maybe I'll do it earlier.
Also, my map is now fullbright because I haven't bothered sealing it yet, the outside areas have no sky for instance. Could the amount of faces (i.e the ones pointing out towards the void that would otherwise not be rendered when the map is sealed) contribute to the error at hand?