Hello, i faced such problem. I added a few items with ContentTweaker to my modpack. I easy added these items, applied textures, even added recipes to special machines from other mods. But when i tried to add a one crafting table recipe there was a problem. There is recipe:
recipes.addShaped("salthide", <contenttweaker:salted_hide>, [ [<contenttweaker:trimmed_hide>, null], [<minecraft:dye:15>, null] ]);
JEI shows me that recipe is avalible, /ct syntax also told me there are no problems, but when i try to fold this recipe it just do not crafts output item.

with items not from the ContentTweaker everything works fine

Without a log I can't tell you much.
However, be sure that the script where you add the recipes runs during the crafttweaker loader, not the CoT one

your recipe form like that
[T ,-]
[d ,-]
(T : trim , d:dye, - : blank)

so it need one blank slot at right side
than its working
[T,-]
[d,-]

[-,T,-]
[-,d,-]
[-,-,-]

but its not working
[-,T]
[-,d]

[-,-,-]
[-,-,T]
[-,-,d]

also your recipe need 'what craft' and don't need 'where i place' than use "addShapeless"is better work.