You may find that this is just how illustrator renders the raster image and when you actually output the artwork that the end result is as it should be. Here is a post on a similar issue: Placed high res bitmap in Illustrator not smooth, but jagged
I just did a test with a .png transparent background image and looked jagged on-screen but when I outputted it as a pdf it looked fine...?
I just think illustrator doesn't process raster very well..?
I hope some of this helps, sorry I can't do anymore.
someone in the post also states a good point that if you embed the artwotk it can then make it difficult to make any changes, etc.