The last time I looked at that I believe the logic is too early when the transparent property is set to true, it goes out and defines the colors then.
What should be happening is prior to drawing the image, it should check the Transparent property and then go out and get the color needed via the transparent mode which by this time should have already been set. So, if it's in auto, it will get the color from the lower left of the image, otherwise it will get it from the color field, whatever it is at the moment.
As you have seen, the Transparent property must be last because that is when it goes out and sets up the color values, it shouldn't be setting nothing but the Transparent flag and that's it.
As I said, prior to drawing, is when these fields need to be examined and setup and allowing other properties to be set in any order.
It's a confusing mess and I have no idea how long it's been there.
Jamie.