If you installed v3.1 before entering Amkethran, I believe it should be okay. The mod doesn't check for her class either, so I don't think the "Improved Archer" mod has an impact.
Looking through his script and dialogue, nothing really pops out at me. I believe I could make a small change to it, but I'm unsure if it would fix the problem. If you have a game saved after you kill him and if you have access to the console, could you type in:
C:GetGlobal("QI#EncounterTalk2","GLOBAL")
And let me know the output of this command?
Also, I made a portion of your post a spoiler, just in case anyone happens to be peeping at it and they haven't played the mod yet.