The symlinks problem can be mostly resolved by adding this magic incantation to your Vagrantfile:

      # to allow symlinks to be created
  config.vm.customize ["setextradata", :id, "VBoxInternal2/SharedFoldersEnableSymlinksCreate/vagrant", "1"]  

That said I have had times where npm via a putty window refuses to install modules. However, I also have npm installed on my Windows box so I can just drop down into a cmd window when that happens and run the npm command there.