In the quest "Doing Duncan a Favor" you are given the choice to either kill 
Koan, or decide not to do so.

If you kill him, you get Pandora's Cube and may return to Duncan for a reward.
This works fine.

If you let him live, you may return to Duncan and (paraphrasing) he says, "Oh, 
that's a shame."
This works fine.

If, however, you tell Koan you will not kill him (so Koan gives you his 
reward), then kill Koan afterward (with the "Use Weapon" skill) you will also 
obtain Pandora's Cube. This creates an interesting scenario.

With the cube in your inventory, you talk to Duncan and the "I didn't kill him" 
conversation is triggered and the dialog screen closes. If you attempt to 
discuss it with him again (still with the Cube in your Inventory), the same 
thing happens. No matter how many times you try to talk to him, the "I didn't 
kill Koan" dialog is automatically triggered.

However, if you drop the Cube from your Inventory onto the ground some place, 
you are then able to discuss other things. One such thing is, "Here is your 
Cube" for which Duncan then rewards you as if you were giving him the Cube, yet 
after the dialog, the Cube is still lying soundly on the ground. The quest is 
completed, but the Cube is not taken (as there is nothing to take from the 
Inventory).



So in a nutshell the order of events is:
1.) Instigate the "Doing Duncan a Favor" quest.
2.) Say you'll take care of Koan.
3.) Go to the Forgotten Bunker in the desert where Koan resides.
4.) Tell him you will not kill him.
5.) Koan rewards you.
6.) Kill him anyway afterward (using "Use Weapon" skill).
7.) Obtain Pandora's Cube.
8.) Report back to Duncan (with the Cube in your Inventory) and witness the 
conversation loop.
9.) Drop the cube, and witness the new choices.
10.) Get rewarded. Check the ground and see the cube still there.


My suggestion: Instead of trying to write a bunch of if's/else's for "if cube, 
reward, remove cube (properly), else, blahblahblah," etc. -- Just make it so if 
you decide NOT to kill Koan, the quest is completed, and if the quest is 
completed, those lines of dialog with Duncan never get triggered.