By default, when you add a Silk Rectangle in the PCB view, it is centered around its position. (Shape Start is set to -5mm 5mm , and Shape End is set to 5mm -5mm ) When you then select it and type a different size into the popup that appears in the PCB view, it shifts so that its position is now in the lower left. (Shape Start will be set to 0mm 0mm , and Shape End will reflect the size you enter) Sometimes the position is shifted to match, sometimes it only partially changes. (the last time I did this, it centered the shape horizontally but not vertically) I would expect changing the size to change Shape Start to -size/2 -size/2 and Shape End to size/2 size/2 so that the resulting shape is still centered. As it currently stands, if a shape is no longer centered, it will shift when flipping it to the bottom layer.
