As an additional information, I un-installed Avast before writing this post just to make sure that it was not the reason for security center disabling.
Please download AdwCleaner by Xplode and save to your Desktop.
Double click on AdwCleaner.exe to run the tool.
Click on the Scan button.
After the scan has finished click on the Clean button.
Press OK when asked to close all programs and follow the onscreen prompts.
Press OK again to allow AdwCleaner to restart the computer and complete the removal process.
After rebooting, a logfile report (AdwCleaner[S0].txt) will open automatically.
Post logfile will also be saved in the C:\AdwCleaner folder.
Note: You need to run the version compatibale with your system. If you are not sure which version applies to your system download both of them and try to run them.
Only one of them will run on your system, that will be the right version.
Double-click to run it. When the tool opens click Yes to disclaimer.
Press Scan button.
It will make a log (FRST.txt) in the same directory the tool is run. Please attach it to your reply.
The first time the tool is run, it makes also another log (Addition.txt). Please attach it to your reply.
It does not allow me to choose this file. Attached a screenshot.
I should be having all the possible administrator rights, or then I'm missing something.
Should I go and run the FRST fix before solving the virustotal thing?
About this file, can you copy it to another location, and then try to upload it to Virustotal. If you fail to upload it, archive it, and upload here...
Now uploading to Virus Total worked!
And it seems one of the checks found a trojan:
https://www.virustotal.com/en/file/bad7e8e226b43f482bb8f3487fe73e5d7e6429d6c2cb0d8292f249e0d65a2d3b/analysis/1385919828/
About MSE, read this and decide yourself --> http://www.pcpro.co.uk/news/security/384394/microsoft-security-essentials-is-designed-to-be-bottom-of-the-antivirus-rankings
Please download DelFix by "Xplode" to your Desktop.
Run the tool and check the following boxes below;
Remove disinfection tools
Create registry backup
Purge System Restore
Now click on "Run" button. Wait for the programme completes his work.
All the tools we used should be gone.
Tool will create and open an log report (DelFix.txt) Note: The report will also be stored on C:\DelFix.txt