Transparency in indexed images is not supported by Illustrator
If you place an indexed image (linked or embedded, it doesn't matter) that has transparency, the transparency is always drawn as white.
If you convert the image to RGB and re-place; transparency is rendered properly. The main problem is that many users will not be aware of the difference between indexed colour images and the alternatives.
eric wiedemann commented
Same thing happens for me when creating an object with gradient transparency and when I use the blend and duplicate tool I get white as transparency as well.