Literally what title says,

ProjectE for some reason looses a major amount of EMC values from various mods, when JEC is installed along side ForgeEssentials.

Removing JEC everything works fine PE+FE work perfectly fine. I am not sure where the problem lies but the issue is there.
Referencing all issues made for your information

sinkillerj/ProjectE#1230
ForgeEssentials/ForgeEssentials#2075

I need to confirm this bug is caused by me and I'm sorry for any convenience I have caused.
I have successfully located the problem. It should be solved soon.
Thanks for reporting it to me

Can you elaborate on what is causing the issue? It is really weird.

@MaPePeR I did some reflection to make black dye in botania able to be used as an ingredient in the recipe. I get the item for dye from registry and forget to check the result. So I added an itemstack with a null item into the recipe. I think this will heppen whenever an itemstack with null item is used.

The latest update seems to have fixed the issue, i can see lots of pages with items when i search "EMC:" in NEI. Approx 6000 items or so vs 2000ish before

Oh, that is really a good news to me :)