If you are using Hauptwerk's built-in MIDI recorder it's working as it's supposed to. It records stop changes but doesn't show the corresponding piston. It's possible that you might be able to see the piston events in an external MIDI editor.
I believe Hauptwerk's MIDI recorder works like this so that playback would be identical on another computer. So if you played back the MIDI file on a friend's computer, and he had the same sample set, the registrations would be identical. If registration was dependent upon piston changes, the effect would vary from one installation to another - your friend might have set up his pistons differently.