Windows is not recognizing all 6 cores and threads, its only seeing 2 cores and 2 threads? is this a common problem or is there a way to fix this?

Could be an issue with the BIOS, Windows, or the CPU. If you update your BIOS to the latest non-Beta release, update Windows completely (and install the FX patch that doesn't come up in Windows Update), and you can't access more than 2 cores, it could be faulty and in need of replacing under warranty.

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I managed to sort this out by going into the bios and turning on all cores manually they now show up in windows with 6 cores and 6 threads do you recommend i install both these updates? do they have any increased performance or such? these are the FX updates i think if not could you link?

http://support.microsoft.com/kb/2645594

http://support.microsoft.com/kb/2646060