Hi Nick,

On my Tyros, I setup & tested out the Tyros 'Registration Sequence' feature (covered on pages 128 & 129 of the Tyros owner's manual) exactly the way you described:

Reg+ : Pedal 2
Reg- : Pedal 3
Seq End set to: TOP

and cannot duplicate the problem you're experiencing.

When I press Pedal 2, the red box (current reg selected) moves back one, and when I press Pedal 3, the red box moves up one, as it should. The red box does NOT later disappear (as in your case) after pressing Pedal 3, even after waiting several minutes.

My suggestion is to try reversing the pedal 3 polarity setting to see if this solves the problem. The polarity setting for each of the 3 foot pedals is set in the Controler Window: Function> Controller (D button). Scroll down to pedal #3 using the 'B' button on the side of the LCD screen, and then switch it's polarity by using the 'I' button as a toggle.

If this doesn't work, perhaps you don't have the latest Tyros OS update installed. The current version is: 1.20 and can be downloaded here:
http://www.yamahapkclub.com/tyros/download/os_verup/os_verup.htm

Good luck. Keep us posted.

Scott