Sounds right to me - when you're entering the setup mode the speedo will stop working while you're setting the end points.
Press the setup button for 3 secs and I believe the red light will flash. Press the set button to establish neutral. Press full forward on the tranny and then press the set button again. Pull full back on the tranny and again then press the set button to get full brake. Let your throttle on the tranny go back to neutral and give the speedo a second or 2 to settle, and then you "should" have your settings stored and a fully functioning speedo.
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