Hi, Willa. You said: "I’ve mixed hundreds of batches of royal icing with the same recipe and brands of ingredients and never had this issue!" So I am curious what you changed this time. There must have been something?? Can you think back to what you did differently this time - as that is likely the culprit. It sounds like you tried changing everything but the brand/type of food coloring. So maybe try a new brand? Or, as Econlady said, maybe you just need to try a fresh bottle of it.
I sometimes see streaks in highly saturated colors that reappear as the icing sits, but if I stir it well and then flood, the streaks generally work themselves out (I assume as they get pushed through my piping cone) and aren't a problem on the cookie.