It is the old Adobe zoom problem when I exported the drawing and viewed it in Acro I got the same bottom line shift as you got. When you zoom in on one of the rectangles the shift goes away. What I would suggest that you do, as there is no need to create a bitmap copy, is to go into the custom settings and choose either PDF/x-3 2002 or2003 as this handles transparencies much better. It also relates better to AI and Acro better maintaining groups, masks ect. Also have a read of the help files in this area it gives a much fuller explanation than I have done but basically it does what Steve did by rasterising the area in question but automatically and you can set the dpi to what you want. As you can see in the screen shots there is no real difference
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