If you check the button mapping in Device mode (under Device > Settings > Customize Buttons), you will notice 2 sets of commands for navigation:
Set #1
DirectionDown
DirectionLeft
DirectionRight
DirectionUp

Set #2
Net/UsbDirectionDown
Net/UsbDirectionLeft
Net/UsbDirectionRight
Net/UsbDirectionUp

Also the device default mapping for the navigation hard buttons are:
Up ----- TuneUp (also mapped on the Rewind button)
Down -- TuneDown (also mapped on the Fast Forward button)
Left ---- DirectionLeft
Right --- DirectionRight

You need to do some clean up here (Device > Settings > Customize Buttons), and decide where to map these 2 sets. You may want to map one set on the hard buttons and the other set on the soft buttons. It's also possible that set #2 also works in regular mode (like in the setup menu) - give it a try.