What version of InDesign are you trying to run with El Capitan?
There is a known bug in El Capitan when you have Auto Show/Hide Menus in System Preferences > General. Turn it off if it is on.
Yeah I am using El Capitan Steve but I have unfortunately tried turning off the show/hide menu!
This is an issue I have had for a couple of months pre changing to El Capitan.
You didn't ask my question: What version of InDesign are you trying to run on El Capitan?