i have never seen the game re-use my planets i have named, no clue why this would happen. I have never completed a game so far, i always seem to restart at some point.. so no clue if it is suppose to work that way or not.
as for the main settings, I think default was something like common, stars, habitable planets, planets, Abundant for asteroids, and anomalies. tight clusters, tech rate normal, extreme planets occasional. Perhaps.. something around those lines..
there could be possibly a user.config file someplace that you could delete to reset it. if you do try something like that, be sure to back up the file just incase.
perhaps someone else can help more later.. GL