Similar thread a couple of days ago, and we couldn't cure it. I'm starting to think it's anew bug introduced with the latest patch, but it may also be a software conflict.
Updated to El Capitan, issue still persists (even with the same document), also a few other problems which sucks valuable seconds from my workflow. Can't be sure if it's the MacOS or Adobe software. Anyone know any way to keep your import/place file window large? (Dealing with long file names all the time), so it gets quite annoying having to extend the window constantly as it always defaults back to smaller size. I feel like Macs are just iPhone/iPad accessories now, not really designed for professional use anymore, they just focus on making the interface more flashy.
Also Acrobat gets worse with every update. Used to be able to create an action, pin the button to the menu and then done. With each update they want to add another mouse click to your process. Also that extra window I have to close to get the the application behind is infuriating =1 mouse click again. Also cannot add 'close file' to an action. For an application that deals with PDF's primarily, it's pretty shocking.