Are you on HW 6? If you're running HW 4 or 5, the directions on page 115-116 of the 6.0.1 user guide are not correct for earlier versions due to an added feature. You'll have to use the version 5 user guide. Email support@hauptwerk.com to request a copy. The quick story is that for v 4 and 5 you only turn on the Scope button and press each divisional piston to define its scope to the currently on stops, couplers, trems, etc.
For v 6, the setter is used with scope now, and the previous process just displays the currently defined scope of the piston instead of setting it. Nice to have!
If you are on 6.0.0 or 6.0.1 like I am, when I follow the directions by pressing the Scope and Setter buttons on the large registration window (not involving my console), they both stay lit and defining the scope works as documented. Please test that on your touch screen or mouse without pushing any pistons on your console to make sure you can do it.
When I use my setter and scope pistons on my CMK3 keyboards, I have to make one change to the directions. My setter piston is hold-and-release, not press twice to toggle the setter on and off. I have to press my scope piston to turn scope on, then press and hold set, press the first divisional scoped piston to define its scope (all per directions so far), then *release* and re-press set to define the scope on each divisional piston instead of holding set throughout -- if (and only if) the divisionals I'm defining scopes for are on the same manual as the set button. I assume that's an interaction in the CMK keyboard itself, but it's easy enough to do it.
(Apologies for inserting myself -- I'll pretend to be "or anyone" for now since I'm no Martin...)