I could not find anything about this after doing a quick search here, but my LT seems to exhibit this weird behavior when using spillover mode. I am on 3.01 and I am using the snap/preset footswitch layout.
I can change presets without issues. But when I am changing scenes, the sound changes but footswitch LED seems to be stuck with the last chosen scene. The color display screen does not update either. However, when I move the joystick (just move it randomly, like moving a mouse to wake up a computer screen), the footswitch LED updates and goes to the correct scene.