I was playing my big 'flagship' game last night, and it kicked over to 5-second time increments. I wasn't sure what was going on, so I let it run overnight on auto, during which time some order finished. I started it again, and then left for work. When I came back, it had stopped again, so I used the designer password to see what was going on. It turned out that the star swarm mothership in a system was trying to destroy a buoy I'd left on a JP, but couldn't because it was out of weapon (though not FC) range. For an hour and a half in-game, it had tried to kill this buoy, and failed to move in. It was sitting on top of one of my wrecks, which might have caused the problem.