It might help to see a screen shot. Could you set the zoom to where everything is up as close as it can be while everything is still in view and take a screen shot. Then, could you take the transparency off of the object and take another screen shot at the same zoom? Post screen shots with the camera icon in the forum.
When you add a transparent object to a page the doc's Transparency Blend Space is use to display the page. So if it's the default CMYK, RGB objects preview as they will convert to CMYK and grayscale objects preview as they would print on the CMYK black plate. You get the equivalent of turning on Overprint or Separation Preview.