Are you flood filling on a new layer with no other art/pixels on that layer? Or are you flood filling on an existing layer with art/pixels on it? If you're doing the latter, then it will flood fill patches of color already existing on that layer -- i.e., if you click on a spot, only that spot and any other connecting areas of the same color will be filled with your foreground color.

To paste to a new image, after copying, hit Ctrl-N or Command-N to create a new document. It will have the same dimensions as your selection. Then hit Ctrl-V or Command-V to paste.