After I upgraded to El Capitan, File -> Recent Projects is empty. Well, 95% of the time to be precise. It worked once for a day or so.
Wow, it did help. My El Capitan update did resent that general setting. The confusing thing is that in other programs like word and excel ‘open recent’ still worked, just Scrivener complied. 
Office probably may use its own recent files system. Microsoft has a tendency to not make much use of Mac infrastructure in their software. You might have seen the effect in a Mac native program like Pages though, or even TextEdit.