So before my aunt left we ran an indigo vat and dyed some cotton yarn. The yarn was a pale creamy yellow when we started, and now it’s sort of a silver gray. We dipped it twice. You can see it in the middle, there. What on earth happened? 
The only thing I can think of is that the yarn didn’t have long enough to presoak (but we gave it a couple days of soaking!) or perhaps it had some sort of chemical in it, which would be odd because it was supposed to be organic cotton. Queer.
And to make things queerer, take a look at the picture. All these yarns were dunked twice. The one on the right was actually dunked three times. Notice anything odd about the color intensity? The brightest yarn (on the left) is a) superwash and b) soaked longer than the one on the far right. They’re both merino wool. Apparently the length of soak time does effect yarns… but the cotton soaked every bit as long as the superwash!