list of mods:
CraftTweaker-3.2.13
NotEnoughItems-2.3.82-GTNH
ContentTweaker-1.0.5
ModTweaker2-0.9.10
CodeChickenLib-1.1.8
CodeChickenCore-1.1.11
Fluxed-Core-MC1710-1.0.9

zs script:
import mods.nei.NEI.hide;
import minetweaker.item.IItemStack;

NEI.hide(minecraft:stone);

fml-client-latest.log
fml-junk-earlystartup.log
latest.log
minetweaker.log

Shouldn't it be

import mods.nei.NEI;
NEI.hide(<minecraft:stone>);

?
Also this is not about NEI but CT.