The update has now been released:
http://universesandbox.com/forum/index.php/topic,82.0.htmlTry running Universe Sandbox again. It should ask you to update.
Regarding the odd orbits:
The trails of the moons around Jupiter are relative to the Sun (well almost).
Right click on Jupiter and select 'Set to Center' from the Jupiter Commands panel to make the motions and trails relative to Jupiter. The only thing that this changes is the way the simulation is drawn. All of the gravity calculations are exactly the same. You can now see that the moons are orbiting Jupiter in circular orbits.
Let me know if there's still and issue or if you have any problems updating.