Hi there @Yoshiken,
It sounds as if your mount isn't being displayed properly in ruTorrent due to the plugin used. If you are using a /home mount you can disable or enable the diskspace plugins per your need. You can do this in the Plugin Menu on the left side of your dashboard panel.
You can then navigate to where you see the plugins diskspace and diskspaceh. If you have a /home mount, install the diskspaceh plugin, if /root mount diskspace
With that set, you should now have the space showing properly within ruTorrent.
This is called reserved system blocks. basically, linux by default devotes 5% to the root system. This keeps your system from becoming completely full and causing a potential lockout of your server. It's a linux design... I know... the more space you have, the more it takes for reserved blocks to avoid a system panic