Not sure when this started, but I begin to notice that every time I start Safari, the same tabs would open even after closing them before exiting the browser. This seems to be recurring across other apps. For example, Quicksilver would always ask me if I want to read the update log for the new version, even though I had clicked "Ignore" many times before. Vox (music player) would always bring me through the start-up introduction even though I have completed it the first time. Some apps would always trigger the "Allow apps to control your computer" even after having approved it many times over. I tried the following: Clearing out the ~/Library/Cache folder and restarting. Did not work. Repairing disk permissions. Did not work too. Exited one of the above apps, deleted its preference files, open it again. Did not work. Hope someone could provide a solution!