I used 100% organic cotton balls from Wallgreens. When I boiled the same water, then poured it into a bowl and let them soak, they didn't turn the slight yellowish color like they did boiling in the pot, so I don't think it's the water. I'll try with a larger pot on medium high and report back. Thanks guys!
And Agavehound, yes I boiled them a few times. The first time, some parts had a slight yellow tone, then with each subsequent boil, more areas turned yellow. Since only certain parts on the outside of the balls turned color, I'm thinking it may have been too much heat in a small pot, thus they may have been "cooking" by touching the bottom in some places. I'm trying it now with a larger pot and will report back in a few minutes. Thanks again!