EDIT
I have reread what your question was asking and I want to ask, is the theme not being enabled at all or is it not setting it as the default theme? If you want it to be your default theme you will have to use a different command than drush en. You should instead drush vset admin_theme theme_name. Here is a link below:
http://www.paulbooker.co.uk/drupal-developer/command-lines/changing-sites-default-theme-and-admin-theme-using-drush
I will leave my vagrant information in case that is helpful to others too.
Could you provide us with the error you are receiving when you try to use drush? In the vagrant folder (where you specify vagrant up) you need to call
vagrant ssh
to ssh into your vagrant and then go into your proper site directory where drupal is installed. Without a drupal instance drush will not exist.
If you are using VDD for your drupal vagrant development, I would recommend following this tutorial on drupal.org:
https://www.drupal.org/node/2008792
Let me know if you have any other details on your issues or any more questions.