When I tried to implement the JEI plugin for my mod, I got confusing results when I tried to add the slots for my machine category.

In the IGuiItemStackGroup interface init() is documented as using position x and y relative to the background texture.
When doing it like it was mentioned there, my slot was always 1 pixel off on x and y.

This is the code I am using when setting the values as actual positions. You can check the texture at the bottom:

    @Override
    public void setRecipe(IRecipeLayout recipeLayout, EnergizerRecipe recipe, IIngredients ingredients) {
        IGuiItemStackGroup itemStackGroup = recipeLayout.getItemStacks();
        // output slot
        itemStackGroup.init(1, false, 65, 9);
        // input slot
        itemStackGroup.init(2, true, 5, 9);
        // set ingredients defined in setIngredients()
        itemStackGroup.set(ingredients);
    }

After looking through my code, there was no other value which could modify that so I realized JEI probably assumes slots are 18x18 pixels instead of 16x16 because it also counts the gray borders.. So I have one pixel less on each axis.
And now this works:

I don't see anything which could affect these positions besides this so I am sure this is the case.
In case you wanna check out the background texture I am using, here it is:

Minecraft: 1.16.5
Forge: 36.1.23
JEI & JEI API: 7.7.0.99

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Thanks for the report!
This is a legacy behavior, clarified with a workaround in 9086768