PCI 16x runs at 1x

Lately I have noticed that all my games have been performing like crap. No matter what settings used I still get FPS of about 30 with drops to the mid-teens. Running several monitoring programs I found out that neither my CPU, GPU or Ram was ever pegged above 75%. I turned to CPU-z and found this:


There is no setting in the bios for this. Every driver, firmware, and bios is up to date. Recent hardware changes have been a 320GB HD with Vista and upgrade to 4GB ram. At first I thought it was vista related, but I went to vista 64 because I thought something was wrong with my 2 year XP Pro SP3 32bit install; but the problem is the exact same. The hardware changes took place when going to vista, so I don't think it could have been that. Also all firmware and Bios have been the same for about 2 months with the last one being just a DVD drive firmware update.

Specs:
Gigabyte DS3 P965 Rev.1
E6400 B2 @ 3GHZ @ 1.375V
4GB Ram 667/750 4-4-4-10 2V
HD4850 512 Core: 625/725 Ram: 2000/2300MHZ (Not overclocked yet since going to vista)
X-Fi Xtreme Gamer
Western Digital 320GB, 500GB Samsung Storage Drive
550Watt Antec

Its set to auto. I tried my system at stock and my pci-e at 110 and 120mhz.

OK I have some new interesting developments.
Default is F13 Bios

1. Installed F11 bios, does nothing.
2. Install F14B bios, does nothing.
3. Max pretty much all voltages (excluding ram and cpu) and underclock to 200mhz FSB, does not work.
4. Install old XP SP2 cd with no drivers, check cpu-z and its still 1x.
5. Took card out installed on bros computer. Bros computer reports full speed 16x with HD4850 (Driverless). I rule out the card as being the problem.
6. Ok I am worried its my mobo. I take his 8800gts and put it in mine. The 8800gts reports a full 16x (Driverless).

WTF???

So far I have gathered that all of the sudden the HD4850 and DS3 are PMSing with each other. Later I will put the HD4850 back in my computer to see if they have made up yet.