Hrm. You could be right (and definitely would be now that I've gotten in the habit of moving my guys manually), but I know there have been times when somewhere was 3 weeks away and I plotted a path to it, and 6 turns later I'm all "Hey, shouldn't my colony ship be there by now?" and it hasn't moved. Maybe I'm somehow killing the autopilot path sometimes though.Anyway, your answer has given me something to think about. I'll pay more attention next game and if it still persists, I'll come back with more info. Thanks!
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There are also two bugs that might be interfering. Both are pretty well known and there are workarounds. The first is the autopilot bug where some ships will lose their autopilot commands after a save and reload if they have movement points left. Two workarounds are to move your ships manually before saving the game and the other is to reissue the autopilot command after the reload.
The second bug has to do with rally points. Ships can lose rally point commands at any time during the game, but usually at the end of a turn. Ships with rally point commands can also be inadvertently sent to a corner of the screen on a random basis. One workaround is to use an autopilot command to a non-rally point. Another is to use the governor screen to reissue the rally point command from the rally point to itself just before hitting the End Turn button. In other words, if you have a fleet rally point named "Rally1", select the "Rally1" point on both the left and right sides of the screen and select "Update".
When issuing autopilot commands, you can select multiple ships by pressing the SHIFT or CTRL key and then dragging a box around the ships you want to move. This makes it a lot quicker. One ship will move immediately and the rest will follow during the End Turn sequence.