The problem was mostly solved... There is one issue I have found - when one (could be two, doesn't matter) of the separations is unchecked and you're zooming in and out, you can see for a moment all the separations, it's like those were all set to on.
We have released a patch that fixes the Output Preview rendering issues that were recently introduced. If you are not already updated to the latest patch, simply open Acrobat and visit Help > Check for updates to apply this patch.
The problem still exists. I zoom in (I'm on OS X 10.11.5) and the separations still show the colors (in this case Pantone 293) even when it's unchecked. It will change too depending on what zoom level I'm at in Acrobat. If I'm zoomed out it's correct but as soon as I zoom in to inspect it's all wonky and can't trust it at all. I'm went to updates and it said everything was up-to-date. Here is the details of my version:
Since the update last week, I can no longer view separations correctly. It sometimes will not work at all. I uncheck each color and nothing happens. Other times I will zoom and out alike you and things will intermittently disappear and reappear not necessarily the right colors either. This all worked before. I'm not sure what to do.
The latest update was a complete and total mess that should never have made it out of the Adobe labs. They should be ashamed and embarrassed at just how shitty Acrobat DC really is. Welcome home Acrobat XI. I've missed you.