I had a computer running Windows 7 Professional that had these problems:
- Certain USB devices were not being detected; specifically, an USB drive was not being detected properly and the driver was not installing and an USB Wi-Fi device was not working properly.
- The Wi-Fi device may or may not be broken.
- File permissions were changed for key folders; specifically, the permissions for the Windows folder and subfolders and the user folder and subfolders.
- I could not change the permissions to the Windows folder and subfolders.
- Microsoft Security Essentials was disabled.
I first suspected a rootkit such as TDSS. So I went into the repair console and tried the commands bootrec /fixboot and bootrec /fixmbr. For good measure, I also tried bootsect /nt60 sys /mbr /force. But this computer had an UEFI and not a BIOS, so the bootsect command does not work. I then tried the System File Checker both with Windows running and from the recovery console. That didn’t work either.
Because the problem was fairly recent, I also tried System Restore. That didn’t work because most restore points were corrupted and the ones that did work would no longer let me log in except in Safe Mode. I received the message “The User Profile Service failed the logon. User profile cannot be loaded.”
After all this trouble, I suspected a virus or malware. So I removed the hard drive and scanned it with my Eset Antivirus. That found nothing too.
My best guess was that some malware that was removed somehow someway before I received the computer took actions to make life miserable. However, at no time could I find any trace of malware. Saying it was malware is only a guess and I have no proof to back it up.
Instead of messing around with it, I decided to do an in-place upgrade. This was a small risk only because just recently Windows 7 Professional was put on the computer as an upgrade from Home Premium. This worked for almost everything. The USB Wi-Fi adapter is still not working properly. This may or may not be because of a bad Wi-Fi adapter.
As my personal opinion, the one feature I wish Microsoft would give us is the ability to perform an in-place upgrade from DVD again (like it could be done in Windows 2000 and XP) and for the product key and activation to be preserved when doing an in-place upgrade.
Update 1: The Wi-Fi USB adapter did not work in another computer either. Either the adapter is bad or it needs the CD. Also, some security updates are not installing.
Update 2: The Wi-Fi USB adapter was definitely defective and the more I think about it, the less sure I am it was a virus. I also remember that this computer had a backup with Windows Home Server but after spending hours trying to reinstall .NET 1.1, 2.0, 4.0, and 4.5. If .NET ever becomes damaged again, it is easier to reinstall Windows than to fix that. Before performing any in-place upgrade, be sure to uninstall all the .NET installations.