To me it looks like there are several issues;
1) Node 60 should not be tripped if you have the Cube, but have decided not to
give it to Duncan (node 68).

2) If Koan is dead (i.e. npc_dead("Koan")), Tux should tell Duncan, regardless
of Tux's possession of the Cube.

3) If Koan is dead, Tux should not have the "koan_spared" cookie. It can be
removed as part of the logic for #2. 

Also, the logic on node 60 could probably use a bit of work...