Nuts. I think I keep banging my head against the wall with this and the best answer is just to be patient and wait... but I never was patient.

I haven't tested it enough to be certain but in three trials of 5 sets of combinations where the items where duplicated once in the original file and once in a new .txt file, it alternated between the two recipes. When I created five new recipes each with the same two inputs but a different output, it randomly returned outputs, based on about the same number of trials.

But I'm wondering if it's possible to override that behavior? Does anyone know if we have access to what is making decisions about whether to look at it's original information verses the mod files?