Ran the app and it said my temp files were in the wrong place. So, I clicked on fix this and logged out as requested. When I logged in again, problem still there. Then I ran into a problem with Microsoft Outlook 2013 not being able to create a temp file in the temp directory. I had to click on the notification 3 times before I could get back into Outlook 2013.
What build version of TP are you experiencing this on? TP versions after July 29th RTM are apparently better. So not sure why you ran into this problem except if the App Troubleshooter kemical linked you to is buggy. Since you fixed it with an OS reinstall, that could be one possibility. Did you remember to disable ALL antivirus, antispyware, personal firewall, antirootkit programs running on that TP build prior to running the MS App Troubleshooter?