I noticed this almost from day one I got my new Mac Pro. 1) Sometimes windows of applications don't jump to front when you click them. You then have to use e.g. Apple+TAB to choose the app. 2) Sometimes windows don't minimize when I double click them. 3) Sometimes the "close, minimize, maximize" buttons in windows are greyed out. 4) Sometimes the menu line shows that you are in an application (lets just say Safari, for arguments sake) but you can't enter the drop down menus. Seems like the OS is "stuck" between applications, until the application is activated). And right now when I am writing this, nothing except Finder wants to activate the menus. When I choose an app the menu bar changes to show the apps' menus, but they don't work. I logged in and out my user, and everything worked fine again. Am I alone with this? It is a pretty fresh install of OS X. I did install shapeshifter, which I uninstalled again though, but apart from that, no "funky" applications. Apart from this things seem to work fine, so I can't blame hardware or anything, luckily.