When I posted this question, I was not sure how to state the problem succinctly and was about at my wits end with frustration.
Basically, whenever I have multiple windows open, I move the mouse outside the window pane I am working with, it disappears into the background and one of the other window pane's I have open appears instead. This was causing me to only have ONE window open at a time.
In addition, I could not access the Start/Shut Down. It would just disappear. (I had to use a work around to shut down) Crtl alt del and click on the red box in the right hand corner. Which worked fine but was not the norm.
After many hours of running unnecessary scans for virus this that and the other (don't bother doing that because it is not that serious), I finally came across the answer on the web.
I wanted to share it here just in case someone else has this issue, it will save them some time and frustration.
I am running Win 7 64
Open the Control Panel, and type "mouse works" into the Search box in the upper right and hit <enter>. On the resulting screen you should see an item called Change how your mouse works. Click on it and on the next screen, scroll down and find the checkbox for Activate a window by hovering over it with the mouse. Just uncheck the box.
One good thing came out of all of the scanning and cleaning. I found I had none of that scary stuff on my system.
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