This is because the 512x64 image, when padded out vertically will not fit in a 512x512 image. It doesn't need to be padded when it touches the edge, and this will be fixed in the next release. For now, a quick workaround, seeing that your images are static images - use sprite dicing on the tall thin one, set the dice size to 64x64 or something like that, and it'll fit in am much smaller texture overall.