I think it's getting confused by what you're giving it.
You're specifying that it needs three of item ID 2 and one of item ID 6, but you're also telling it that it needs 3 of category 'Runes' and 1 of category 'Runes'. The category option overrides the individual ingredient option, so it doesn't matter what ID you set there.
Category ingredients are for being more vague in your recipes, so this likely isn't what you want at all, given you have given names to the runes you used. Get rid of the category and see if it works that way. Right now, the recipe is set to need 3x 'runes' and 1x 'runes', meaning it is looking for 3 items in the runes category and one item in the runes category, not the green or grey rune specifically.
What I think has happened is that your rune items don't have a category on them, because you didn't use that note tag. The recipe, because it has categories set, is ignoring the item ID part, and is only looking for runes, which these likely aren't. You'll want to remove the category from the recipe.
Alternatively, you could add the <craftCat: Runes> note tag to those runes, and the recipe would probably also work, but it would work with any items in any order, like 3 grey runes and a green, or 3 red runes and a green, or any other combination of 3 and one runes items.
I'm also not sure, but the DQ mode might require you to set the ingredients one by one instead of putting a quantity. So you'd set the recipe as green x1 green x1 green x1 and grey x1, instead of green x3 and grey x1. You probably want to change that back to normal mode, because that's not what most people want.
~Ramza
