My Pilot Droid used to keep flying my Cap ship in sublight, even if I undocked in my Freighter. Now my pilot droid keeps piloting even if I'm abord my Freighter inside my Cap. Once I undock, travel aborts.

Is this something new with the pilot droid, or is it a bug?

"Droids with piloting skills can maintain travel after the pilot has left the ship or vehicle (such as by entering a docked entity), therefore avoiding a potentially annoying and unplanned abort."

You may enter a docked entity and your droid keeps course. But if you leave your ship he stops. Plain and simple.