CEP's Sparky Spawner should not be messing with regular encounters. It runs off a completely different system. I actually use a mix of both it and regular encounters in my PW.
Sparky Documentation: Sparky Spawner: Tips, Tricks, & Troubles
My guess would be that it's something to do with your removal of factions. Have you done a full "build" of the module since you took them out, after doing an "updated instances" on all of the encounters you may have updated in the pallete? Not much, but it's the only advice I can offer on this topic.
Actually, after spending countless hours today trying to figure it out, I finally opted to restore my module to an older revision. It wasn't the CEP 2.4 encounter system causing the issues, it was the removal of the factions in general. Correct me if I am wrong, but NwN sets players to the PC faction by default right? And you use the faction sliders to indicate who is hostile and who is not? Ironically, the module we're using as a base actually assigns a sub faction to the existing faction. When Jesse ripped out the factions and changed that code, it broke just about everything.
I never did do another full build, didn't realize you had to if you changed the factions. I did do an update tho, since it's forced after that change. In any case, it's working again, lost 10 hours of hard work in the process, but lesson learned.