The custom field option of the core plugin or all the custom fields configured using the custom fields addon should show up in the checkout popup window.
Custom fields is the ONLY way to add any fields to the checkout popup. Otherwise, you will ask for one field and someone else will ask for another field and so on. The custom fields addon allows us to give a solution that should work for a lot of our users out there:
Are you using the NEW API option in our plugin?