One more slight issue with this. It needs to be made that when you set a new course using Navigation or Nav computer that the long range course set on the star chart is erased. This was not the case on one of my ships. I set a simple course back to Sol and set it on auto pilot. The ship was near sol and I wanted it to jump while I was offline. I didn't realize it still had a course set to the wormhole that leads to the giant star cluster. This is a location it had automaticly had set when I was having that one bug before and carried over from another ship. So my ship followed that itself and ran out of fuel partway there. This was pretty annoying.
OK, here is what I see that might have happened:
You had a chain jump set up and wanted to explore another location and then wanted the auto-pilot to jump you there (the new location) when you were offline. It did just that. And since you were off-line (sleeping, etc.) and not setting another task for the ship, auto-pilot re-engaged (while you were offline) to finish the jump criteria in your computer. You need to set the 'long-jump' chain to the new target and then go offline. If you are on-line, it doesn't matter (you can adjust the ship movement manually).
It's kinda a case of 'paying attention to where you sent your ships'.