I recently used Sky Safari to simulate Callisto's occultation of Ganymede on April 17. To do this, I had to set the time about 40 minutes early, which is the same as the light travel time from Jupiter. Not including the light travel time means that the positions of the moons will not be the same as seen through a telescope. The software is showing their positions as they will appear 40 minutes later.
feature request: light travel time for planetary moons