Summary: Spellcheck in QuarkXPress 2016 allows you to re-visit the Last Skipped words during a spellcheck session; and the skipped suspected words can then be spell checked again.
Also the spell check is now restricted to visible layers only which means textboxes on visible layers will only be searched for spellcheck. To do spell check on hidden layers the layers should be made visible.
Solution:
To do the Spell check Navigate to Utilities >> Check Spelling.
The option for Last Skipped will only get enabled once a word or few have been skipped during the Spellcheck Session.
This option will get disabled again once all the Last Skipped words have been visited for that spellcheck session.