I did want to mention that one way I've found to work around these kinds of problems is to browse to the Manager page >Site > Machines, and remove the problematic machine from the site. Then add it back in. If something has gone haywire, this normally helps smooth it out. Though as a warning, if things are not working correctly to begin with, you may find yourself with the machine removed and difficulties adding it back in.
As a result, I normally recommend to anyone with a 10.2 or newer server to take advantage of the backup functionality before making any changes to the server. Here are the docs for this as well.
http://resources.arcgis.com/en/help/main/10.2/index.html#//015500000666000000 - Linux instructions
http://resources.arcgis.com/en/help/main/10.2/0154/01540000065s000000.htm - Windows Instructions