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Power Surge, Computer Only Boot if CMOS Battery Taken Out

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I have had a computer for about 2 years (2TB hd, Gigabyte MB, radeon hd 5700, amd 6 core cpu, 4 sticks of 2GB ram) and never experienced any problems. Two weeks ago we had a storm here and there was a power surge that lasted a few seconds. My computer was plugged into a power surge protector but it was not an expensive fancy one, more like a power strip with a fuse. The computer would boot to the windows 7 screen where the 4 colors are spiraling and come together and once finished, it should have went into the page where you would select the user. Unfortunately at this point, a blue screen would appear and it said terminal error. I looked up the hex address and couldn't find much information on it. So I went ahead and reinstalled windows and then I got it back to booting up like normal. I started installing drivers and such and when I rebooted, the computer did not beep (usually beeps once a few seconds after pressing power) and the display would not kick on. Fans and lights are on, but it just sits like this for a few minutes and then shuts off. I messed with it, thinking it was the graphics card, and the only thing I found that works is wait about 10 minutes with it plugged in but the power off, or to take the cmos battery out for about 2 minutes and put it back it. When I do either of these two things and press power, the computer will beep and boot like normal. I can reboot several times before this happens again, but never fails to come back. I have noticed funny things such as the computer stalling and lagging (thinking) more than usual at times, as well as the sound stuttering at times. I have installed new drivers for video and sound, have not messed with bios updates or anything. I have a hard time believing its the PSU because it does work at times. But waiting 10 minutes seems like something is either cooling down or discharging. And taking the cmos battery out just for a few minutes I believe is clearing the cmos, so sounds like the MB may be bad. When it was working for a while, I took each ram stick out and booted one at a time, booted fine over and over. Before I start replacing things, does anyone have any ideas what may be the problem. Thanks for your input.

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