Newly (created by Drupal) dir not writable after first upload?
It's the server software that controls the file permissions, you need to have that set up correctly first. Drupal is then granted access to the dedicated folder for site uploads and other generated files necessary for the site activity. 

It's very important for your site security to have the files' and folders' owners, groups, and permissions correctly set up, and this is a part of any Drupal installation. 

This is a long but detailed resource on this: Securing file permissions and ownership 

Usually you need to make the www-data user the owner of the files/ folder, this is the Apache server user on a lot of installations but YMMW, it can be called something different. And it's important to give all the necessary permissions for that user and the group too, but not more than necessary to keep it perfectly secure. 

Doing this step during Drupal installation usually ensures you don't stumble upon file-upload-permission related issues. 

Also check your Status Report for any messages related to file uploads. You will also have entries in the Latest log entries if the system encounters something worth throwing an error for. And check the File system related admin pages (under Configuration), try saving the form there and see if you get any errors and get more info about your case.  

Did you use some special Drupal Vagrant setup?