That's what I'm thinking too. Windows should have installed an update that somehow messed with something else.
Right now I'm having the slowdown. Deleting two folders with a few files each took almost 2 minutes. I have task manager, resource monitor opened and nothing peaks or seems wrong. Every other program behaves normally if it is open. If I launch a program, it will take a few minutes to open and work slow.
I will take a look at the Microsoft Answers forum and see if someone has already reported this. I'm almost sure that an update is the culprit.
I ran sfc /scannow and it found no integrity problems
I wondered if it was an AV but then realised I only have default Win 8 defence running, no 3rd party,
Feels like something is deeply scanning the files before giving you access right :?