Comment 4 for bug 602651

It doesn't seem to be related to the actual inversion method, since the pixel operation is very straightforward and is applied the same no matter if there is a visible layer beneath it or not. Also worth noting is that the image preview in the layer list and open images list will have transparent pixels turned white even if they're still transparent on canvas. (Even if you only have a single layer.)

This leads me to believe that something is wrong with how layers report their colours to tools other than the canvas. The reason all the transparent pixels are turned white is because the inversion tool is being told they're black (while the canvas has been correctly told they're transparent), and then subsequently orders all the pixels changed to white which is then passed on to the canvas.