After doing some more testing:
1)I cannot repro the problem with the programming you are having, so I don’t what else to suggest.
2) Programming the right and left arrow keys on the jog wheel for scrolling track may not be a good solution after all. Because of the silly focus/key command problems in Nuendo, the right and left arrow key commands behave differently depending on which window is in focus. If the Project window is in focus, you need to use Up and Down arrows to properly scroll. If the Mixer is in focus you need to use the left and right arrow keys to scroll. So you would need to program 2 different soft keys to scroll depending on which window you want to scroll in.
So what I thought would be a great solution for you, is only a partial solution.
However I have a soft key programmed to scroll plugin list windows with the jog wheel that works wonderfully.