I assume that you're using Apache as the webserver on your VPS.

Maybe some/all of the modifications made in de .htaccess aren't allowed by Apache.

In the vhost configuration of Apache make sure you have the following in your section where you configure the Elgg vhost.

<Directory "/path/to/elgg/installation">
    AllowOverride All
    Require all granted
</Directory>

Also check the Apache error logs they may give you a hint what's wrong