I'm running Windows 8.1 x64 (Verssion 6.3, Build 9600). Starting yesterday and ever since (despite restarts and so on), my windows have been almost-constantly behaving as if they are set to "always on top." At first I thought this was limited to Google Chrome, until I noticed practically every window (Visual Studio, Outlook, Notepad++, HipChat, Remote Desktop instances) was behaving this way.
Following advice from this question (pressing
ctrl+alt+esc to remove the "super state" from a window, restarting explorer.exe, etc) provide temporary fixes, but it doesn't take long for the problem to resurface again. Unlike that question, though, my problem is not caused by use of "Show Desktop." It just happens.
What on earth is going on? This is a very frustrating issue.
UPDATE: It very may well be Synergy that's causing my issue, not Widnows (as the KB update is not on my machines but it still happens, and force-closing Synergy from Task Manager makes the problem go away).
UPDATE 2: Since Synergy was my cause, I have selected an Answer for this post. However, as pointed out, if you don't have Synergy there are other potential causes of this issue.