Depending on which "FixIt" tool you ran - you might have already rebuilt most of the SoftwareDistribution folder.
If it was the FixIt from here... How do I reset Windows Update components?
...then take a look at the "Let me fix it myself" section.
I've never had a issue letting the OS rebuild the entire folder...
But - I have a Windows 7 box that is failing to install the 3 updates that you mentioned at the start of this thread and rebuilding the entire folder did not help.