Your setup (minus the VM) is very similar to mine.
Mine differs thus:
VS Pro 2013. (Loving Resharper also!)
No VM.
No Virtual Box.
It has worked fine for all Revit 2016 service packs.
I'd hazard a guess that it's the VM fogging things up. Check to see if the non-updating file is locked. (Right-click & Properties.)
Have you looked at the Revit journal to see if anything is reported?
Have you checked that the linked project is actually getting rebuilt? And copied local?