Have you done the pinout mod on the PCIe extenders? Poke around the forums, something about voltage you need to bump up or short out or some such. Can't recall exactly, I'm not using ribbons myself.
For some mother boards you will have to short 2 pins on the 1x slot to get it to work. I had to do this, but I find it strange that you're 16x slots won't work.
Here's the blog that details this,
http://blog.zorinaq.com/?e=42