basing off my experienced its based on npc id.
You have zone A, and npc B with id 1001, and a script attached to him.
If you spawns this npc in ANY other zone, where he doesn't have a default script for THAt zone, the script from zone A will trigger. (if it does have a separate script per zone, and still triggers wrong scripts- then I don't know what is wrong)
The BEST way to avoid this issue, is have similarly named npc in the other zone under different ID, and assign script to np ID rather than his name. (1002.pl instead of John.pl)
I may however be wrong on all accounts =)
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