Diane,
I don't think it's a conflict. There are different types of posts to your wall, and not all of them show up in the Fanbox. Things you type into the wall to share will always show, but things that get pushed to your fan page from other apps may not. It's completely up to Facebook what will push to the Fanbox and what won't, and there's little we control of that.
Hope that helps you explain, but definitely test with different wall post types to see what works, and I think you'll get it under control.
Thanks,
Alex