I was having the same error message. I couldn't get Windows Update or Microsoft Security Essentials to update.
After resetting my router. Going from wireless to wired. Resetting the wireless repository. Connecting to a different network. Scanning my machine with the Malicious Software removal tool, Microsoft Fixit, Malwarebytes, and AVG nothing come up as a found problem.
Checked the host file. Proxy settings.
Reinstalled all the patches that were installed the last Microsoft updates that installed, it still didn't work. I was stumped.
The only other thing that I noticed on my machine, was that "some" google links were being directed. I ran hijack this. And still no issues found.
Then I tried tdsskiller as to solve the google redirect issue.
It found and cured the file C:\Windows\System32\drivers\nsiproxy.sys
I rebooted. And boom! Everything was fixed. WUS and MSE both update now. And my google redirect is fixed.
Just wanted to share that after 3 days of trial and error, it was fixed with TDSSKiller from <cite>kaspersky.com</cite>