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Ged, have you noticed that the longer rectangle on the bottom also act's in the same odd manner as the smaller one? You can use the Direct Selection Tool and alter the path of the rectangle, but you always have the odd underlying path and shape. It also copies itself. Very strange......................I really would like for this oddity to be solved.

Also, in the OP's psd that I downloaded does not have the path (made with the Pen Tool) that your showing.