Closed Game does not completely reset when I create a new character

Greetings Chucklefish community,
I have recently upgraded the game known as Starbound to version 1.3 and due to this then I have decided to delete my current character and start a whole new game. Everything seemed to be functioning perfectly until I got to "The Ark" and noticed something very peculiar. It seems like the quest based NPC's that you meet in the verity of different quests are still at "The Ark" even after I completely restarted the game. Worst of all, the gate to "The Ruin" is still open which defeats the point of the entire game due to the fact that I am now able to enter the ruin after the first 10 minutes of restarting the game.

Here is an photographic example of this bug: