No he didn't download that, he thought the problem was gone.
Apparently it wasn't when he cloned the drive read his statement more closely.
Besides that I can see why he is desperate to remedy the problem he thought was fixed.
According to this part of his post, it sounded like he did install it:
The only possible connection between this machine and the last is that I had installed Windows Updates Downloader a few weeks ago, though I had not used it to download files. I had inserted a USB stick containing the updates I had downloaded, though I had not opened the folder they are in or run any. I can't find any reports at all of malware associated with Windows Update Downloader. Virus scans come up with nothing. What on earth could be going on?
Though he said he didn't use it to install Updates...it's possible the software itself is somehow corrupting permissions.