You say AE's updated. Is it at least v. 11.0.4?
Yes. It says 11.0.4
I'm seeing now that some people had problems with some adobe software when updating to El Capitan and uninstalled and then reinstalled. So I might try that.
Cool. Some possibilities follow. Not definites... possibilities:
A FANCY MOUSE: For AE work, a plain ol' 2-button, hard-wired mouse with scroll wheel is best. Those wireless jobs and "magic mice" are known to induce errors.
A FANCY KEYBOARD: It's the same deal as with a fancy mouse.
A TABLET: While handy for Photoshop/Illustrator, they can cause AE fits. Tablet drivers are often sources of AE woe.
WEIRD FOOTAGE: I don't care what Adobe says, the simpler and more straightforward the footage, the better. No highly-compressed stuff. No exotic codecs. No pioneering media containers. Image sequences? Great! QT's in standard codecs? Fine! Some transcoding may be necessary.
NORMAL SOFTWARE WEIRDNESS: If your machine hasn't been turned off for more than a day, or you installed something without the benefit of a restart, give it a shot. Doing such things are actually theraputic.