What does Separations Preview have to say about the color numbers? Are they the same?
It shows them all the same. 100 100 100 100 Is there a knockout setting that is replacing the transparent items with a less rich black?
That's registration color and way too much ink for anything but printers' marks, but aside from that your problem is most likely YDB (but without seeing at least a screen shot of the page I can't say for sure). See InDesignSecrets » Blog Archive » Eliminating YDB (Yucky Discolored Box) Syndrome