It's a known problem with CS6 and El Capitan. CS6 is end-of-life and will never be updated. It's not compatible with El Capitan.
Either roll back to a previous OS, or move forward to a Creative Cloud subscription.
I had the same problem and found a solution. You have to install/reinstall the old Apple Java Runtime (Java 6). You can download it here: Download Java for OS X 2015-001
Then you have to restart your Mac. After that your InDesign CS6 will work like a charm again (hopefully ;-)
I hope it helps …