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I don't know if this has been discovered yet but when you open the application icon editor. If you go to erase the original image it doesn't erase it just becomes black. Also you can't color anywhere outside the circle. Here is an example image.
http://www.freewebs.com/gerblegod/problem%20diagram.jpg
The image is pretty self explanatory. The dimensions marked by a blue question mark don't experience this glitch.
It's probably only the full colour (with alpha) versions then.
Not that I know what's wrong, I just suspect it might be because you're only editing the colour channel and not the alpha channel.
Dynasoft is right. You'll have to edit the alpha separatly.
First, click the Transparency button, then check the Edit box.
Then click the Show box. This will show you only the Alpha channel. Anything White is opaque, anything Black is 100% transparent. Gray areas are partially transparent.
just click the New button to start a new image (that's the easiest thing to do when starting from scratch).
Ok, thanks guys. I completely forgot about the alpha channels. I did just hit clear in the end. Well, that clarifies one more problem.