Here is the link to a save right when I think it was beginning happening (I couldn't find the exact instance, the ships are far away from the star and are getting father but I couldn't get them to go all the way out again).
My version is 1.096
If you notice around the blue star, my fleet is pretty far from the gravity well. Now, when I played the whole game through, the ships were even further out (nearly half of the distance to the next planet!). I couldn't repeat it, but maybe this will give you a start?
Here is the save: http://www.mediafire.com/?mwddtxqlnhx
And the stats: http://www.mediafire.com/?oyl1cpcuizd
I'm looking for a more comprehensive replay of it, still watching! If I find a more obvious version of the error I'll send that via email to stardock...