I can reproduce the problem but it’s a bit different than I originally described.
If you set your Game Mode default pawn to be the MotionControllerPawn from the VR template level everything works fine.
If you have a different pawn (say spectator pawn) as your default but in your PlayerController you instantiate the MotionControllerPawn and make that the new pawn the motion controllers will not appear until you restart the level as I originally mentioned.