Odd Window Minimizing Problem

I'm having a very strange issue, and I have never even seen anything remotly close to this..and for some reason this just started happening today.
Problem:
OSX is not allowing me to have two application windows open on the screen at the same time. If Mac Mail is open on the left of my screen and, I select safari from my dock OSX will auto minimize My Mac Mail Window and open the Safari Window.
This goes for all applications.. (Calendar & Mac Finder), (System Preferences & Reminders) etc..
It will not allow me to have applications focused on one desktop screen.
Tech Info:
Mountain Lion 10.8.2
Macbook Pro Retina 2.6Ghz 16GB Ram
No External Displays Attached

Have you tried starting in Safe Mode and see if the problem still occurs?
Restart holding the "shift" key.
(Expect it to take longer to start this way because it runs a directory check first.)
If this works look in System Preferences > Users & Groups > Login items and delete any third party login items (-), you can always add them back with the (+). Also look in /Library/Startup Items. Nothing is put in that folder by default, so anything in there is yours.

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