Have you unticked "Automatically hide and show menu bar" in El Capitan System Preferences under the General Tab?
Having said that CS6 is not supported under El Capitan, you should consider upgrading to InDesign CC2014/2015.
Beyond trashing your preferences, CS6 is not supported under El Capitan and you are on your own.
Perahaps use your back up to roll back to an earlier operating system.
"Automatically hide and show menu bar"
Thats exactly what is was. Just toggling it off didn't work. I had to reinstall CS6. I downloaded a trial of CC 2015 and the same thing happened. Well not the exact same thing, but CC would crash upon startup. Had to reinstall with the menu bar option off to get it to work. That's too bad. Hiding the menu bar is a great feature in El Capitan. Stinks to not be able to use it just to run InDesign.
Thanks for your replies gentlemen.