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.
Best Answer
The answer to this question involves a bunch of things.
Preview/PDFKit in Sierra is just buggy (10.12.5 +.6 Preview Version 9.0 (909.18)). It is less robust in this regard as Preview in either Yosemite or High Sierra. And coupled with apparent auto-termination this is the only 'background process' that really matters in this regard.
Once the bug gets triggered (enough) it is much earlier in Sierra Preview compared to other versions and propagates through the application: that vanishes from the Dock or from the Cmd+Tab application switcher but remains active in the background as Activity Monitor will show. That tempted to reach the conclusion that almost all PDFs were affected at first. But once a
killall Previewcleared that process up for good, only bug-triggering PDFs (that might justifiably called substandard) really triggered that behaviour.But one such concrete bug trigger I could positively identify is related to Multiple PDFs with page group included in a single page warning. It is somehow dependent on the number of these incorrect inclusion attributes but I couldn't determine the exact amount. Since many of my own PDFs, files I downloaded and had to work with and also the given example in the Question above demonstrate: this is a widespread weakness leading to very unwanted behaviour on Sierra, not only but (for me) mostly from LaTeX generated content or many includes for an assembled PDF.
Unless this bug in Preview is fixed, or the PDFs are reflown there is no solution but to avoid Preview on Sierra for these kind of files.
A workaround is to use other applications like Acrobat Reader from the start for all PDFs to display if they contain text.
Once this bug is triggered with Preview, it is necessary to kill all PDFkit related processes since quitting the application Preview via cmd+q or the equivalent menu item is not enough sufficient.