You’re right in that this does not have to do with permissions. You will run into it depending on a particular server configuration. To ensure that you don’t have to deal with it on an ongoing basis, you will want to add the FTP credentials to wp-config.php like so:
define( 'FTP_USER', 'username' );
define( 'FTP_PASS', 'password' );
define( 'FTP_HOST', 'ftp.example.org:21' );
There is a whole section of this in The Codex that explains all the WordPress constants that also allow you to specify SSH keys in the wp-config.php file.
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