When you access the /vagrant shared folder within a Vagrant guest VM, the file vagrantfile is not listed & you cannot create files in the same folder (permission denied / inaccessible).
Virtualbox guest additions on the vagrant box are mismatch from the version of virtualbox installed on the host.
The ideal method would be to obtain a vagrant box with the latest virtualbox additions.
If this is not possible, install the vagrant vbguest plugin which will automatically upgrade guest additions if required at bootup.
Install command to run on the host when running Vagrant version 1.1+:
vagrant plugin install vagrant-vbguest
Once installed, reboot the vagrant VM(s) using vagrant reload / up where relevant, which will install the guest additions. If the /vagrant folder is still empty, perform a second reboot using the same method.
Full installation instructions & additional configuration options are available on the vbguest plugin’s page on github.