Problem: Some applications like Preview or Skim do not display anything in certain PDFs, primarily in text PDFs, while images work fine. Skim even displays tables of contents but both start beachballing heavily after quite a while. The PDFs display fine in Adobe Reader and I do not see anything meaningful in log or Console.
Logs for "Devices" in Console are filled up with messages like these:
Preview the behavior of the UICollectionViewFlowLayout is not defined because:
Preview the item width must be less than the width of the UICollectionView minus the section insets left and right values.
Preview Please check the values return by the delegate.
Interestingly this situation looks infectious. Certain small PDFs open OK at first and keep this state while scrolling. But after opening a larger PDF, which does not display anything, the first PDF degrades its display quality, especially after scrolling. To illustrate this, left is Preview.app, right is QuickLook preview for /Library/Documentation/License.lpdf:
It seems quite weird that this looks more like a collection of bugs in Sierra's Preview.
One bug is that the intermediate scrolling representation in Preview sometimes doesn't get updated properly once scrolling stops. This effect is visible with almost all PDFs but remedies itself rather quickly most of the time.
The worst bug seems to be triggered when using big and complex PDFs especially when they were produced with LaTeX.
One example seems to be this UserGuide. Preview seems to be affected the worst. Closing Preview windows pseudo auto-quits the program but doesn't eliminate it from the list of running processes. Once a document like this is opened Preview.app or Skim descend into an abyss of weird behaviour like in the screenshot above. On other Sierra systems that were less manipulated than mine the same behaviour was observed, but not always. Currently I do not see which systems will be commonly affected nor a pattern for which PDFs will trigger these symptoms.