This issue occurred only for this particular station in a star system of the Freedom faction. Right after jumping to this star system I'd enable AutoPilot for the point in map where the station was, and the AP would show a "autopilot disengaged" message, please see screenshot:
http://www.mediafire.com/view/dv1sb7sgfaok0f2/Untitled.png. The "A" on the radar is the station, it's a straight path from where the jumpgate is (no obstacles).
This issue occurs consistently, after going to a different system and coming back, or restarting the game. Also I noticed if I fly away just a little from the jumpgate, AP would work, it's just in the vicinity of the jumpgate that it wouldn't fly.
I hope this is enough information to find the issue

I finished the game and coming back to the map the star systems are completely different from what I had before.