Someone on his blog actually asked if the extension was necessary. After nuking the old folder, run the update again and all is well but it takes a long time to go through that long download and update process. I have found that the easiest way to fix a Microsoft Update problem is to switch back to Windows Update from the "Change Setting" option on the left-side menu.
In case you are not familiar with it, WSUS is Microsoft's free patch management tool. If you don't know the difference then you don't do Windows support.
OK, here's the main difference: In addition to OS patches, Microsoft Update takes care of your MS Applications like Office, SQL Server and Exchange. WSUS has a good monitoring and reporting feature that allows me to see at a glance which machines are struggling with the stuff Microsoft is trying to send to it.
Additionally, you receive a "0x0000009F" Stop error if you shut down or restart the computer.
Fixes a Windows Server 2008 R2 issue in which AD LDS authentication returns error messages when you try to perform an LDAP bind on an account.
So I do a Remote Desktop session to the machine in question and run the process manually. I used to spend hours looking up ways to get around these errors. This process of switching from the newer method to the older one and then back again seems to fix a host of registry errors and other wastes of time.