Uncle's machine not shutting down correctly.

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My uncle asked me to take a look at his machine. It wasn't booting into windows. I've installed a new HDD and reinstalled Windows and all is well now, except that when I go to restart or shut down the machine, it hangs on the "shutting down" screen. It just hangs there. Nothing happens. It just sits there. I have to manually shut down the machine. Of course, this triggers a disk check on the next boot.

I would like to resolve this issue. The machine is a Gateway DX4860-EF31P. It has a low end Sandybridge i5, 6GB (I know, I know) of RAM, and I have upgraded the included garbage GPU to a GTX 560Ti 1GB that I had lying around. The PSU surprised me by having two 18A 12V rails so I was able to do this. Card works perfectly. I realize I should upgrade the PSU but I'm not into putting lipstick on pigs and this thing won't be in use much longer perhaps 18 months then it's going to the junk yard.

Thoughts on the shut down issue plz? Cheers.
 
Unplug and replug all the cables, remove memory and boot with a single stick, see if that clears up the issue(cycle sticks and slots to see if the issues changes if not gone already). Next step i'd take would be to remove and boot the system outside the case barebones.
 
Unplug and replug all the cables, remove memory and boot with a single stick, see if that clears up the issue(cycle sticks and slots to see if the issues changes if not gone already). Next step i'd take would be to remove and boot the system outside the case barebones.

I'm going to do this later tonight. I've been busy the last couple of days.
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Does anybody have any other ideas? I really need to get this sorted.
 
This'll be a OS issue, not a hardware issue - try disabling auto starting apps & telling the computer to shut down after a reboot.

After that, manually kill apps one by one then tell the computer to shut down - what's refusing to die?
 
On a fresh install? (with a new HDD) Boot in safe mode and see if shutdown still hangs.
 
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My mate had this problem, and it got worse as it would take longer to boot and shut down. And then some times would take a few power on's to get it to go, then we both had a look at it. We found that the sata cable to the ssd was not clicked in all the way, so made it click tight and it was good as new. Hope this helps as it could be many things.
 
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