Have you unticked "Automatically hide and show menu bar" in the El Capitan System Preferences General Tab.
Thank you so much! It works!
Do you know why it does that by the way? I hid the menu to have a clean background but if it will do that to adobe programs I'll just leave it on!
We were able to delete cache files (Mac OS X) for InDesign (without having to reinstall InDesign) to restore functionality:
Restarting InDesign (without having to restart the computer) brought InDesign back.