I believe this effect is due to anti-aliasing. The edge for each layer is half ffffff00 and half ffffffff. This is basically averaged, so each layer has about 128 alpha along this diagonal. When the layers are merged, this becomes about 192 (actually 198) alpha. So there is nothing wrong with the gimp, provided you think anti-aliasing is a good thing. If you threshold the masks, killing the anti-aliasing, all is well. -James Smaby
