I've had this problem for a while now, every time I try to add custom recipes to the SAGMill, they aren't actually added. The current issue is in the Galactic Science modpack (I add some extra mods).

Here is the content of the SAGMillRecipes_User.xml:

<recipeGroup name="GalacticScience">

    <recipe name="ExNihiloBrokenIron" energyCost="100">
        <input>
            <itemStack modID="exnihilo" itemName="iron_broken" itemMeta="0" />
        </input>
        <output>
            <itemStack oreDictionary="dustIron" number="4"/>
        </output>
    </recipe>

</recipeGroup>

This is output in MC console for it:

[18:15:32] [Client thread/INFO] [EnderIO]: Added user defined recipe group GalacticScience
[18:15:32] [Client thread/INFO] [EnderIO]: Removed recipe ExNihiloBrokenIron due to user config.
[18:15:32] [Client thread/INFO] [EnderIO]: Loaded 2 grinding balls from SAG Mill config.
[18:15:32] [Client thread/INFO] [EnderIO]: Excluding 8 recipes from grinding balls bonus.
[18:15:32] [Client thread/INFO] [EnderIO]: Found 57 valid SAG Mill recipes in config.
[18:15:32] [Client thread/WARN] [EnderIO]: Not adding supplied recipe as a recipe already exists for the input: 1xitem.material@3
[18:15:32] [Client thread/WARN] [EnderIO]: Not adding supplied recipe as a recipe already exists for the input: 1xtile.blockOre@3
[18:15:32] [Client thread/WARN] [EnderIO]: Not adding supplied recipe as a recipe already exists for the input: 1xitem.material@6
[18:15:32] [Client thread/INFO] [EnderIO]: Finished processing SAG Mill recipes. 54 recipes avaliable.

Why was the recipe removed? The Ender IO config has no option for individually turning off custom recipes for each machine. And the problem is only with the SAGMill, I can add recipes to the Alloy smelter just fine.

I don't know why in the original issue post, the < SAGMillRecipes > and < /SAGMillRecipes > is removed from the SAGMillRecipes_User.xml content, but these tags ARE present in the file. I actually had to add spaces in this post for them to show up!? WTH

Ex nihilo is registering its ores after the recipe phase. So when Ender IO tries to process the recipe, it cannot find the referenced ore and discards the recipe, thinking it is for a mod that's not installed.

see #1962

is there any way to fix that?

Galactic Science has these nifty scripts (customRecipes.zs) to add custom recipes, could I use that instead?

like this for Ex Nihilo:
mods.exnihilo.Sieve.addRecipe(GalacticraftCore:tile.moonBlock:3, minecraft:blaze_rod, 50);

rewrite to:

mods.EnderIO.blockSagMill.addRecipe(exnihilo:exnihilo.iron_broken:0, ore:dustIron, 4);
or
mods.EnderIO.SAGMill.addRecipe(exnihilo:exnihilo.iron_broken:0, ore:dustIron, 4);

But I'm not sure if that is even possible with Ender IO devices or if I'm using the right name to address the SAGMill.

Ok so i actually tried both and I get an error in MC chat:

ERROR: customRecipes.zs:120 > No such member: EnderIO

...shame.