Usual suspects
Someone (or something, including malware or malware removal) changed the permissions for a given user, try the takeown command http://www.faqforge.com/windows/take-ownership-of-a-file-or-folder-by-command-in-windows/https://technet.microsoft.com/en-us/library/cc753024.aspxhttp://ss64.com/nt/takeown.html
Hard drive is on the way out and you are seeing this.
You changed the hard drive/windows install and caused something like the first one, again the takeown command is what you want to play with.
The files are actually gone, usually someone tried to make a backup copy and moved things instead.
Not so much for everything but if you shared it then it could be all being accessed.
You tried to encrypt the drive/folders with something, such things can happen here.
Some anti virus tried to protect something and is preventing access.