Using the following CTT script:

https://gist.githubusercontent.com/TeetoKaziim/f0714899f46c50a8019bbba93df1a7c1/raw/7f44e46f259d57e6d15735372d425ecd984a15a0/materials_system.zs

No model json is generated in:

InstanceFolder/resources/contenttweaker/models/item

Even with an ore_rubble.png present at:

InstanceFolder\resources\contenttweaker\textures\items\ore_rubble.png

In-game the inventory models for the items in question is a black and pink Square with the text name of the item.

https://gist.githubusercontent.com/TeetoKaziim/f0714899f46c50a8019bbba93df1a7c1/raw/438298504a1bce13bac959aefc253241a8e9a4e3/fml-client-latest.log

Almost forgot I was asked for a log I hope this is the right one?

https://cdn.discordapp.com/attachments/227825847732666368/405607962330267648/unknown.png

Amusingly jei knows what color the items are supposed to be.

So Update:

I wish I'd got back to this sooner: This problem does not reproduce in a "fresh" instance with as few mods as possible. (just contenttweaker/JEI) I need to spend some time tracking down which mod/mods are interfering.

I don't know what happened suddenly it started working for no reason when I tried to track down the mod that was interfering. Closing this. Sorry if anyone wasted time looking at this.