Have u sorted it yet?
I had the same problem and I semi-sorted it by upping my PCI-e freq to 110Mhz, sometimes however I would have to reboot to get the correct x16 link width.
ASUS tech support told me to set PCI-e to 101Mhz and the NB voltage to the lowest selectable value 1.25 (or something like that). I was sceptical and this didn't quite work (no x16 at all), however raising the NB voltage to the next value up (1.4?) and leaving the PCI-e clock the same at 101 has done it - always boots into x16 and I have kept my over-clock at 3.2 Ghz.
This board was very twitchy for the first three weeks but after a lot of tinkering it seems *crosses fingers* stable at last.
Oh....and it flies