System Refresh Removed Programs

I encountered the issue of the computer being stuck on a black screen upon launch. I attempted a system refresh to see if it would resolve the problem. Afterwards, I found all my programs in the Windows.Old folder and brought them back for use. Unfortunately the problem reoccured the next time I turned off the computer, and I attempted another refresh. This time, all of the installed programs were not within Windows.Old, and so I must reinstall them. I do not understand this inconsistency.

Take a look here:
http://www.eightforums.com/tutorials/2293-refresh-windows-8-a.html