Opportunity is missed by most people because it is dressed in overalls and looks like work. - Thomas Edison
Select everything. Go to the Attributes window. You will see overprint fill and overprint stroke. If everything you selected has a over print it will be checked. If there is come items with over fill and some with out it will have a box. Just click the box and it will make it a check, then click again and it will have nothing. Now none of the items selected have over print.
Nick, not sure I quite understand but, "overprint" fill on the attributes palette is so the color on top does not knock out from what's below. So, if Overprint is checked, you should be fine, so that the element prints on the top color film, and the bottom color film, like say yellow with a white underbase. If it's not checked, then it knocks out of whatever is below it, as opposed to overprinting. I can't wrap my head around something marked overprint not printing...Stevewhen you choose an object, use select same fill color to get all of the elements of that color, go to the Attributes palette and see if they are checked or not, that would at least avoid checking each element one by one.
I just had the same problem... actually made it to press before we found it, in the first print...our solution... use spot colors for all colors...then, select the artwork and use the 'merge' feature.that makes all the 'pieces' discreet... with no overlap.