We had this Windows 7 x64 computer come in for a malware removal, and it was not able to download files using Internet Explorer 9.  We cleaned out all the malware, and when I can in the next morning, it was running updates from Windows update.  Shortly after I came into work, Windows Update threw an error 1606.  I, also, noticed standalone updates would install fine, but some Microsoft installer would just hang and never install anything. 

I started checking through Microsoft KB886549, and checking the registry keys; I would have used the Microsoft Fix-It, but being unable to download anything made that not possible.  Luckly, the broken registry key was near the top of the list – HKEY_CURRENT_USERSoftwareMicrosoftWindowsCurrentVersionExplorerUser Shell FoldersAppdata