I can see you have a hell of a lot of layers there - maybe the issue - try playing around on different layers, or the background (or flatten image first).
Take the selection tool, select a square, then use the fill tool (the bucket with paint coming out). Click it over the selected area. Make sure the selected layer is correct.
Try it on the Layer called "background" and if it doesn't work for you there, start a new image from scratch and see if it works there. I've never heard of this issue before, so you'll have something activated!
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