I have seen the same thing. It is rather confusing to say the least, as it is intermittent at best. Also there's issues trying to use default.pl, and I've also noticed that more than 500 quests active in one zone makes some just stop working or not work at all.
As ChaosSlayer said, make a new npc, and rather than A_Quest_Giver.pl, use the NPCID#.pl. Sometimes it will work with the name, but, it is not a guaranteed solution. If you MUST use names, add some numbers in the name, as that will distinguish it. Trakanon_1, Trakanon_2, #Trakanon. The underscore, the pound, and the numbers get parsed out in displaying, but it does signify a unique mob for scripts, and you won't get that nasty crossover.
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