It looks like the ImageList editor loses the transparency when it does some internal copy or clone of the images. However, it seems that it does work when you add the images in code to the ImageList. One workaround (not so tidy) is to add the images to the ImageList at design-time (so that your design-time will be closer to the run-time) and then clear that ImageList and refill it with the images in code.
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