OK, I knew I would get asked this!!
On a Standard RST exhaust manifold, there is a single stud-hole in the middle which is smaller than the rest. Also, the studs themselves have a small shoulder which means that the stud won't pass completely through the smaller hole.
It was done to be a tight fit to locate the manifold correctly. Having weighed up the pro's and con's, I filed the shoulder on the stud down as it makes it so much easier to remove!! I guess alot of RST's have had this done in the past too.
Make sense?