You slash Tobias Durol's jaw, breaking it with a loud *SNAP*
Tobias Durol slams into you and sends you sprawling!
Tobias Durol's bash knocks the wind out of you.
Tobias Durol punches at your chest, you start to cough up blood!
Tobias Durol punches at your left arm, tearing open a big bleeding wound!
You parry Tobias Durol's bare fist!
You slash at Tobias Durol's right arm, cutting a painful wound across it!
Tobias Durol is stunned, but will probably recover.

[HP: 36%] [ME: 22%] [PE: 69%]
The wailing screams of past sacrifices echo into your ears.
Tobias Durol regains consciousness and rises unsteadily to his feet.

[HP: 39%] [ME: 24%] [PE: 69%]
l

Before a large rickety wooden wall with vines intertwined
Weakened by prolonged submersion in the murky waters of the surrounding
swamp, this cypress wall looks to be more for show than actual use as a
defensive position. Thick dark vines entwine their way through the gaps and
holes in the structure giving it a surprising amount of its structural
integrity, without which it might not stand at all. The surrounding ground
is still completely damp despite the apparent receding of the flood water.
Various muddy footprints and markings litter the ground from the new found
traffic treading through the area.
It's raining lightly, hot, and breezy.
Obvious exits: e w
(Charmed) A silver-winged pegasus stands here looking majestic.
A pale male human is here expounding on the virtues of his slaves.

[HP: 39%] [ME: 24%] [PE: 69%]
Tobias Durol counters your attack!
Tobias Durol's counterstrike devastates you.
You slash Tobias Durol's head. Tobias Durol falls with a blank look on his face!
Tobias Durol is DEAD!!
Tobias Durol's head is skillfully severed from his body.
You get 4 gold coins from a corpse of Tobias Durol.
You get 9 silver coins from a corpse of Tobias Durol.
You get 7 copper coins from a corpse of Tobias Durol.
You junk a corpse of Tobias Durol.

[HP: 27%] [ME: 24%] [PE: 69%]

[HP: 36%] [ME: 22%] [PE: 69%]
The wailing screams of past sacrifices echo into your ears.
Tobias Durol regains consciousness and rises unsteadily to his feet.

[HP: 39%] [ME: 24%] [PE: 69%]

I believe that here's your answer. A tick happened, and since the NPC was stunned during the tick, it considers it being out of combat now. Thus, he is able to counter your attack, since it's an attack that you started anew (considering he was out of combat).

Actually, he probably just was unlucky enough to stun him on the combat round right before the tick and was thus still in combat the entire time, indicated by the fact that he was on mode kill.

And it's probably because the NPC can technically initiate combat with 0% PE, but since he got no attacks, the counterstrike trigger remains set and fires when the PC swings back.