Foreground application constantly becoming inactive
I recently ran the update to 10.11.1 after it had been asking me for a few days and now I wish I hadn't. When I am in any application and working, the application will all of the sudden go to the background and it will be "inactive", like another app is in the foreground but there is nothing there. If I wait a few seconds or click on the app I'm in, it will be active again but it makes it incredible difficult do do anything, especially type this message. So many errors because it is constantly going inactive when I am typing (or doing anything for that matter).
I have restarted the computer, checked for additional updates, checked to see if there is another app running in the background that I am not aware of (though the Force Quit Menu and Activity Monitor), ran the "First Aid" in Disk Utility on both the user level and on the computer level though the recovery partition. I have done some research on this and nothing is coming up. I also looked around the Forums a little and nothing came up there either. Sorry if this a duplicate.
I am just hoping to not have to reinstall the operating system if I don't have too, but at this point I'll do just about anything.
This issue has basically made this computer unusable.
Running:
Mac OS X 10.11.1
Macbook Pro Retina 13" (Late 2013)
MacBook Pro (Retina, 13-inch, Late 2013), OS X El Capitan (10.11.1)