Windows Update will at times, it seems, require the system to be shut completely down. Seems some updates, like .net need some extra help. Also, some anti-virus programs can interfere with the process of restarting for update installs.
A startup repair may need to be run 3 times for it to repair problems. Hard to say, but depending on what is wrong, it may ask to be restarted or you may have to do it manually.
If you get a message saying the bootmgr is missing, you may need to run the bootrec /fixboot command.
Beside shutting completely down once in a while, it is also a good idea to run SFC /scannow from an administrative command prompt to check your system. Files are replaced pretty much all the time while the system is running, but running the command directly will tell you if any system files have gotten corrupted and not replaceable.