Walt well, what I have observed, is that the glitch happens most commonly when you have not locked your view onto a ship of yours that is also jumping. Also I have noticed that only the ships go tho the next sector/planet, but your camera stays in the sector you already were.
I think that's a camera glitch... The camera does not always follow your ship.
It can mostly be fixed by locking your view onto the jumping ship (middle click onto the ship).