Have you viewed it in wireframe mode to insure that there is nothing hiding behind the "bottom" layer?
Depending on the complexity of the object, is there anyway to copy each element seperately, and be sure that the item you are grabbing has nothing else with it? In other words, don't drag a box, individually select the item.
Lastly, did you do any editing of the image in PhotoPaint, or some other bitmap program before importing into Draw? It is possible if you edited a portion of the image (especially in Photo Paint), if you had the wrong object selected when masking, cloning, painting, etc, it extends the layer to include the object you are modifying (even if you think it is a different object or different layer) and your modification can appear on the wrong layer or object, even though the change occurs as you intended. It ends up creating a gap between the objects, and you cant move one without the other. This can get translated in Draw as white background. If this happend with a few objects or layers, it could appear as disconnected white squares. You could always edit the image in PhotoPaint since it sounds like it is a bitmap, and look at each element individually - you may find some artifacts you didn't think were there.
The other options come into which layers you are printing. That gets a little beyond me since I don't do it very often, as I try to avoid layers so I dont have to deal with these sorts of anomolies.