C'mon, Adobe! You lead me to this black-hole of a forum, so chime in with some insight. I've got work to do!!
Does this happen in every comp - even in a brand new project?
You could consider updating your OS to the latest. (Is it 10.11.2 or 10.11.3 now?)
The difficult issue sometimes with stuff like this is that CS6 is not officially supported for El Capitan, so I would be unsurprised to find weird issues popping up. However, I know a number of people are using it successfully, so I wouldn't give up hope yet.
Yes, it happens in new and existing comps. It was working fine for the longest time. The best I can figure, it happened after I installed the CC 2015 trial, because I wanted to test it out. Once the trial expired I uninstalled it and attempted to go use AE CS6 again, and now I am having the aforementioned issue. I will try the OS X update and see if that does anything.