Somewhere along the way, your Preferences have corrupted themselves. Rename you current Preferences folder to something like, Preferences Copy or Preferences1. The Preferences folder will recreate itself, and you are set. You will need to reset the preferences for each application. So, for example if you have smooth scrolling turned on in Appearences, or if you use tabs in Safari, those kinds of things will need to be redone. You can also move the corresponding Preference file from the old Preferences the the new ones. If you are not familiar with this, the Apple Preferences are named like this: com.apple.mail.plist for Mail, or com.apple.safari.plist.
That should fix your problem. But if it is a recurring one, you may be in for an Archive and Install, or maybe a clean install if it is at the user level.
Good Luck.