Anyone who has ever had a problem with .NET Framework, particularly a repeatedly offered security update, knows how difficult it can be to fix. Without a specific error code, it is more difficult to research the source of the problem.
Until recently, the primary go-to source for help was Aaron Stebner's WebLog on MSDN Blogs at Unified .NET Framework Troubleshooting Guide. I have also provided the recommendation to install .NET Framework security updates, with a shutdown/restart and separately from other security updates.
The tool may make one or more of several possible changes to the installed product. For example, it may correct the state of Windows Installer on the computer, reset the DACLs on certain folders, or resolve some issues that are related to invalid or corrupted update registration.