MSE Malfunctioning, Windows Update Error C80003FA, and More

A while ago I built my own computer, and it worked fine for about two weeks. However, since then, it has had many errors and problems with programs. After wiping my drive and reinstalling countless times, I've kind of been able to get it to work (I'm using the computer to write this), but I can't do any Windows Updates (it gives me error C80003FA) and Microsoft Security Essentials has gone crazy (can't update, won't scan), so I'm running it without any antivirus. I tried running MalwareBytes, but when I tried to download it, it wouldn't install and told me that the download was corrupted.

I've searched for solutions to the Windows Update Error, and many people suggested restarting the Windows Update service, renaming the folders, etc, and none of it has worked. When I try to update Microsoft Security Essentials, weird things happen. The progress bar goes to the end, but before it's about to finish, it goes back to the beginning and starts again. Then, just before it finishes, it stops and says that it failed to connect and can't update. Also, when I try to refresh the Windows Experience Index, it errors in the middle of the assessment and closes.

I don't know what could be causing these problems, my best guess is some sort of virus, but that doesn't make sense either as I've wiped the drive multiple times and flashed the BIOS as well (just in case it was something in the BIOS). Any help would be appreciated. Thanks.

kegobeer said:

Where did you get your drivers? Did you install any drivers?

I downloaded the motherboard drivers from the MSI website, and the graphics card drivers (Catalyst Suite 12.6) from the AMD website.

Jacee said:

Make sure that IE proxy settings are disabled ...
1) Under “Tools” in the browser tool bar select “Internet Options”.
2) In the “Internet Options” window that pops up, click the “Connections” tab at the top.
3) Click “LAN Settings” near the bottom of the “Connections” section.
4) If the “Proxy server” checkbox is marked with a check, click it to deselect/uncheck it.
5) Click “Ok” to close the “Local Area Network (LAN) Settings” window.
6) Click “Ok” to close the “Internet Options” window.
Reboot
Make sure "Proxy server" is still disabled under your LAN Settings.
Test whether internet connectivity is restored.
Also, see this Windows Update error 80244016, 8024402f, or c80003fa

If all was working okay up until a day or so ago, then it could possibly be malware causing a 'connection timeout'.

I can browse the internet using IE, but I can't download or install anything internet related. I've tried installing Google Chrome, Adobe Flash Player, Java, and none of those work (they error at some point during the install). I have a feeling it is some sort of malware, but I don't understand how it could survive because prior to installing Windows 7 this time I wiped the SSD using DBAN (Darik's Boot and Nuke), and I flashed the BIOS (just in case something was there).

Would replacing the motherboard make a difference? Because I've already replaced exchanged the RAM and also bought another set, and I've wiped the SSD and nothing has been fixed. I don't think replacing the CPU or the GPU would help, so this is the option I'm leaning towards. I've thought about taking it in to a computer repair place, but I don't want to go there and have them tell me "Yep, this needs to be replaced, and here's a $50 service fee" when I could have just replaced it on my own.

I found this....it may help.

Windows update error HELP C80003FA - Guru3D.com Forums

bassfisher6522 said:

I found this....it may help.

Windows update error HELP C80003FA - Guru3D.com Forums

I've seen that before and tried the things they suggested, but they didn't work. I managed to download MBAM today without it erroring, but the scan I ran came up with nothing. I then tried MSE, but the same things happened and it still didn't work.

I just ran TDSS Killer, and it found 43 threats (all medium risk). They seem to be regular windows processes (i.e. wuauserv.exe), but it says that they are forged files. I looked up some of them, and they seem to be related to some of the problems I've been having, so maybe these files are the problem? Should I delete them, or quarantine them, or ignore it?

Yes....delete them....