With Asus latests P35 gaming boards, the Blitz Extreme and Blitz Formula, which are using an IDT chip to give you two x8 PCI Express slots instead of the normal x16 and x4 configuration of the P35 chipset, a problem has occured on the Asus FAQ.
It seems that the second slot is PCI Express 1.0/1.0a only and according to Asus, this older PCI Express standard isn't compatible with PCI Express 2.0.
The primary slot is PCI Express 1.1 and it doesn't have this problem as this version of PCI Express is compatible with the upcoming 2.0 standard.
So what's the significance of this? Well, it means that you won't be able to use newer PCI Express 2.0 cards with several motherboard, not just these ones, as if your board has a 1.0 or 1.0a PCI Express slot, a PCI Express 2.0 card won't work in those slots.
So much for the new standard being backwards compatible...
You can read the Asus FAQ here