Just a question for OP.
After using the Fixit program, the Windows7 update program would be expected to again inform you that the updates have not been installed yet.
Did you actually hit the install button to allow the download and install take place? Letting the computer take the needed time to install, and then hitting "restart" with extra time allowed should work this time.
The fix program may have worked removing a bad install. Although; in less you actually shut down the computer during the install, the computer would not have installed any marked "failed". A warm "restart" is not the same as shutting off the computer, and then starting up again a little while later. That is a "cold start"
Windows7 saves a backup point right before the install. The computer program will automatically revert to this point for a failed install. This may be the case and the reason the fix program found nothing wrong after rechecking again.
There are times when a certain update might fail on a retry or two. One of the Silverlight updates was one from about two years ago. The update can be checked and "hidden" so the reminder does not keep coming up. I left that one "hidden" for a few months, and then "unhide" it to allow another chance at installation. It worked that time since they finally got the bugs out.