Recently tackled my wife's vista sp2 laptop that wouldn't install a kernal level update from last Feb 2011. Research showed probably fault of an infection of some kind in deep.
First TDSS Killer found TDSS.tdl3 on it. Updated fine then choked on three of them from Dec 2011.
Reasearch seem to show another infection of somekind. ComboFix found and removed the zeroAccess rootkit, even told me it was in tcp/ip stack and might have net access trouble). Got that monster out of there but then even running manual updates failed with a new message...
"error 0x80096001...system level error verifying trust"
Ok back to Google......and tried MS and other (not many) fixes I could find and came up nothing.
Saw your Windows Repair tool recommended on Major Geeks for use after severe malware infections. Figured what the heck....downloaded and ran 11 of 22 on custom (internet access was not damged). While I still couldn't run Windows update from the site I could do manual installs
Should I run the full repair? I'm thinking its a Internet Explorer problem now.
Thank you for getting me that far, this definitely goes on my rescue thumbdrive.
Oh, and donation made.... this is a super tool.