With some mobos, you have to short some pins to make the x1 extender work in a x16 slot:
http://forum.bitcoin.org/index.php?topic=30831.0See the third post.
Be careful, though, as some have reported frying their boards doing this. I would order a x16 --> x16 connector, and maybe do the short trick while you are waiting for it to arrive (if you really want to mine this way in the meantime).