I've done some experiments with that bug (can't leave starbase), and it appears to only occur after combat in another star system (not Alpha Draconis). With auto-save off, I went to the next star system (Beta Draconis), did nothing there, returned to base, and I could leave just fine. Went to that same system, got into combat, returned to base, and then the bug occured.
Hope this helps with debugging. I love the game.
 "4D Maze"){kind=icon}
 "Drunken Masters"){kind=icon}
 "Starcom"){kind=icon}