htaccess rewriting itself wrong

Every 4 hours or so my .htaccess file gets overwritten, it should be

# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ – [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]
</IfModule>

# END WordPress

BUT what I get is these two lines being put together like this;

RewriteEngine OnRewriteBase /

This then causes a 500 internal error on the site and the only way of me fixing this is every 4 hours going in and adding a line break, can anybody advise as to how I can fix this? I have 9 other wordpress installations on my server and none of the other sites which are all upto date are doing this.