Okay, just for the simple fact that you can in fact assign lanes, I would think that you have an older (i.e. Pre2008) MacPro. That's what I have and it works great.
You need to put the card in slot3 and then setup your PCIe config to option number 2:
http://www.aja.com/html/support_xena_boards/exp_large.htm
Again, you need to read this page carefully about how to configure a
Pre2008 MacPro
http://www.aja.com/html/support_kona_rec_sys.htm#
Jeremy