Motherboard freezing in bios and flash screen

System specs:
Gigabyte motherboard Z68-D3H-B3 (Intel socket 1155)
C4 60gb ssd (OS)
WD Black Caviar 650gb HHD
Antec HCG 640m
GTX 560
G Skill 2x2gb 1600
I5 2500k
Windows 7 64bit

So here’s what I’m running into, I was getting BSOD message “A clock interrupt was not received on a secondary processor within the allocated time interval” so after reading up on the error I tried two things. First I rebuilt the PC and updated the BIOS (from F5 to F13). After I completed the rebuild and updating the bios I started running to problems were my PC would freeze up on the motherboard flash screen or in the bios themselves. Occasionally it would load into Windows, but would ask me to run Startup Repair which in most cases would freeze up again. I mainly only have my OS on the SSD so I reinstalled Windows 7 (disconnecting the HHD during the install). Once I was able to get Windows to reinstall, updated the drivers, the freezing continued or in some cases the system would just keep rebooting (I would hear the beep, nothing on the screen, than it would reboot again).

I then loaded BIOS version F12 and the same issues kept occurring. So I went to BIOS v. F11 and finally able to get Windows install, drivers updated, anti-virus, all was good. I used the system for about 5 hours no issues. I go to power down at the end of the night and Windows closes, but my case fans continue to run. I don’t think much of it until in the morning and the fans are still running. I manually power down and power it back up and get the message to run Startup Repair. I hit enter and system freezes up again. I use the Windows 7 disc to try and repair through the disc and freezes when loading files.

Any other suggestions I could try? Roll back to a earlier BIOS? Is my motherboard on its way out?

The motherboard still under warranty so hopefully Gigabyte will honor that if the problem is due to my motherboard. Now I do only have the OEM Windows 7 64bit so if I do get the motherboard replaced will I need to repurchase Windows 7?
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  1. Quick update. I spoke with support for my motherboard and gpu. i went ahead and removed my gpu and all but one stick of ram. System booted fine. Added my 2nd stick of ram and system booted fine again. Ran memory test (Prime95 Blend test) for an hour, no errors. Reinstalled the gpu in the PCIEX16 slot and issues returned. I installed the gpu in the PCIEX8 slot and no issues. Assuming the issue is with the PCIEX16 slot and will work with Gigabyte on that.

    I also noticed that my PC will sometimes no power off. Windows closes but my case fan continue to run. My BIOS are set to default so don't believe that it's a power management issue. So tonight i'm going to disconnect everything from the PSU power it on/off and see if the PSU fan continues to run, my assumption it may be a bad pin.
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