@kdfrawg This was with a downloaded & pre-annotated PDF. Any annotations I made and any that had been done pre-download had been stripped out. Turns out there's major PDFKit problems with Sierra- apparently Apple concentrated too much effort into getting PDFKit to work with iOS 10 & the Sierra variant just got fucked up.
Some sources report that the issues are rectified in macOS 10.12.3 beta.
Looks like I'll have to reclaim the 2008 El Capitan MacBook Pro from Mum's place. I keep it there as a convenience and because it's limited to a maximum OS of 10.11, its PDFKit is unaffected.
// @jws