Cannot switch between applications by clicking on open window

I am using a MacBook Pro, OS X Yosemite V 10.10.2
When I have multiple applications open, I cannot click on an app window to use that application. (this includes clicking on files the desktop when not in the finder app) I can use other means of changing applications such as corners or gestures.

Please read this whole message before doing anything.
This procedure is a diagnostic test. It’s unlikely to solve your problem. Don’t be disappointed when you find that nothing has changed after you complete it.
The purpose of the test is to determine whether the problem is caused by third-party software that loads automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.
Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards, if applicable. Start up in safe mode and log in to the account with the problem. You must hold down the shift key twice: once when you boot, and again when you log in.
Note: If FileVault is enabled, or if a firmware password is set, or if the boot volume is a software RAID, you can’t do this. Ask for further instructions.
Safe mode is much slower to boot and run than normal, with limited graphics performance, and some things won’t work at all, including sound output and Wi-Fi on certain models. The next normal boot may also be somewhat slow.
The login screen appears even if you usually login automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.
Test while in safe mode. Same problem?
After testing, reboot as usual (i.e., not in safe mode) and verify that you still have the problem. Post the results of the test.

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