WordPress Security Check breaks Wordpress

I have experienced this with Plesk 12.0 and now also with 12.5, so I thought maybe I should report this.
When I use the Security Check tool for Wordpress and I put the checkbox on "Security keys" and click on "Secure", it displays an error message. Then, the website does not work anymore, because wp-config.php is completeley blank, 0 bytes in size! So I need to restore that file from backup. Very annoying.
This affects basically all Wordpress installations on the machine, no matter which one...

WordPress Security Check breaks Wordpress