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When I try to choose a fill color it will not change and stays with a ? in the box? What does this mean and how do I fix it
What do you have selected and what are you trying to fill? Please include screenshots.
I believe you may actually select multiple objects with different Fill properties (colours or no fill).
You can see in the expanded Layer in the Layers palette what you are selecting.
What happens if you deselect and Click the (Fill within the) desired object with the Direct Selection Tool?