Forge: release 1.16.5-forge-36.0.43
JEI: 7.6.1.71
CraftTweaker: 7.1.0.135
Create: v0.3e

When a Crafting Table recipe is added Create automatically generates an Automatic Shaped/Shapeless Crafting recipe for it.
However recipes added using CraftTweaker do not show their Automated Crafting recipes in JEI, but do work in-game.

Here's an example recipe added using CraftTweaker:
https://pastebin.com/EgCt5y3g

Notice no Automated Shaped Crafting recipe visible, however the recipe works fine in-game.

Here's an example of what it should look like:

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Thanks for the report!
Please report this to CraftTweaker: https://github.com/CraftTweaker/CraftTweaker/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc
Jared probably has a better idea of how this works than I do.