Mobo Power, Reset, and BIOS_A LED's stay on after I shut down.

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This isn't a new pc build, I've been using it for about a year now and everything was fine until yesterday. I installed "A-tuning" and fiddled around with some stuff (The operation mode, good night LED, and fan-tastic tuning)

Also, something out of the ordinary I did was try to install a "modded realtek audio" - followed this website: http://www.digit.in/forum/tutorials/175047-realtek-driver-mod-creative-x-fi-realtek-chip.html

but I deleted/uninstalled all that crap because I realized none of it was legit. For clarification, the reason I was trying to do it was because I got new headphones and they weren't loud enough and someone said this would fix it.

Anyway, what do these lights mean? How do I turn them off? I can't remember if they were always on or not, were they?; I might be paranoid lol.

Thank you.
 
Solution
Ccleaner (get the portable version) will clean off any unnecessary files from your PC. Run windows to make sure you don't have a virus. Other then that you are good to go.

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The only weird thing that occurred was when I restarted my pc, just the taskbar and my wallpaper poped up and after about 5 seconds, everything else popped up.

I have no idea what I did. Could it have been a virus or something that installed into my pc with those files I installed?

Oh and something I noticed is that my bois isn't up to date. But i'm guessing it's been like that for a while, I doubt that that's the issue
 

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hm.. okay i'll try that.
I'm running windows defender right now, is that necessary or should i just cancel and install ccleaner and do that?
 

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ok thank you. I ran ccleaner, now I'm running the windows defender scan. I will report back after the scan is complete.
 

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Alright, it scanned, and there was a virus, "virTool:Win32/Obfuscator.XZ" with a severe alert level.

However, after removing that, and restarting my pc, the lights still stay on