I know one thing that has been suggested, is to offer a second nesting box if you have the cage space. The thought is that she'll use the one as a potty box, and keep the other clean for nesting. I find that it's mostly my first timers that do it, and once they give birth they stop. I also find that it's mostly my Californians that do it, and most often it's when they end up not being bred. I have one cally doe right now who has been doing nothing but pooping, and saturating her box with urine. She's on day 35, so I'm taking it as a sign she didn't take this time around.
Another thing to consider, did you put the nest box in a corner of the pen where she typically doesn't poop or urinate?