Hi Samantha, I would try to give your starter a few days of feeding at room temperature, taking care to feed it when it's at its highest point of rising or just beginning to fall. This type of feeding routine will keep the wild yeast active and should result in your starter rising and doubling predictably. If you're seeing that kind of behavior I doubt that your starter has succumbed to  any unwanted invaders, and the color you're seeing is more likely a result of the type of flour you're feeding it. 

I hope this helps! Let us know how it goes. 

Barb

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