Aha,
I have been having very similar issues on April 19, 2016, my OS is win7 x64 sp1
First I found my win update took forever to find any updates(it failed), after I cleaned some win update backups files, I got into an infinite configure windows 35% loop at login. Couldn't get into my system.
All system restore failed. Had to use DoS to recover.
Then I used Tweaking.com's repair to fix win update, afterwards it could find updates.
However, after successfully installing 30+ updates, I'm stucked with 4 failed updates:
1. An IE 11 update, but I have already got latest version, that's why it failed to update with error 9C48. From the log, I see "A newer version of Internet Explorer is already installed on the system". SURT and Windows Repair could not fix this problem. I guess the only solution is to reinstall IE 11.
2. KB2574819 successfully installed, but it reverts back after each restart... I ran SURT, after 3 hours, this problem was fixed.
3. The Feb 2016 security updates KB3126593 and KB3126587 failed with error code 80070490: error not found. SURT didn't fix this problem, nor did Windows Repair.
Microsoft Fix It never fixed any of the above issues...