I think I know how this lag happens. If the star system wasn't mapped out, I could autopilot fast enough without dropping my FPS. But after I mapped all the stations in that system, it gets lag every time I start autopilot. This occurs when the objects on the map are enormous such as asteroids and stations. Mainly on large map such as earth space ice asteroids system.
I kinda suspected this caused by the new feature of station list that have been introduced in version v1.9 (or v1.8?).
...that hypothesis would explain why starting systems like Tau Ceti begin with heavy lag: they have large concentrations of stations near nav beacons that light them up immediately.
I've made a couple of fixes that should reduce/eliminate lag. Will release a new build soon.