Maybe it's not about finding bad verts. SS sent this to me in a PM: "turn your walkmesh into a poly, select all the vertexes, and hit "Weld". Weld to 0.1 cm, there was a huge difference in the number of verts before and after." Huge lifesaver.
Also, if it refuses to work ingame, it might be that you've decompiled it in order to work on it. I remember having that problem with one of your BoS areas.