I created a macro that deletes the plist files between every excel action and I am still having windows disappear - so I assume the problem has nothing to do with plists(?)

You can open up console application and monitor the activity and see if anything unusual is recorded by this application. You can go to the Preferences of this application and set it to come to the front whenever there is a change.

This would probably be a good place to start.

Seriously doubt it. Excel is to entrenched in the business community. It is that Apple is just providing another alternative to use spread sheet on the Mac.

I found a solution for the great disappearing excel window... at least it worked for me and my colleagues. We all have a third party app called "Noteshare" installed on our machines. It seems that the contextual menu items that this app installs were causing the issue. Once I deleted them, the issue stopped.

Even if you are not using Noteshare, it could be contextual menu items from another 3rd party app. I noticed on some other forums that an application called "Sticky Brain" was doing the same thing.

To remove your contextual menu items, delete all files in the following locations:
/Library/Contextual Menu Items
~/Library/Contextual Menu Items

Thanks - that seemed to be the same issue for me... I had recently installed a Trial version of NoteTaker which is from the same company as NoteShare. And I just noticed this problem with a workbook in Excel...

I uninstalled it and removed both NoteTaker related entries in the Contextual Menu Items folders (/Libraries and ~Libraries)... now the Excel disappearing window problem is gone.

NoteTaker Plugin was the Culprit for Me Too
 

This is a "me too" post. I found this thread by searching for the exact same problem. I followed the advice of pulling the NoteTakerCMPlugin.plugin file out of the /Library/Contextual Menu Items/ folder. It worked right away and the problem disappeared!

I had a weird thing happen. I closed an Excel file. When I reopened it, you could not see the workbook. The icon was not missing. Thought there was a problem like above, however, come to find out that the workbook was hidden by Excel. Had to manually unhide it under Window>Unhide.

Freaked me out for an hour or so.