Hi Andrea,
This looks like a drupal issue, not a cpanel issue and I am not that familiar with Drupal.
That being said, are you sure the above htaccess is the complete file that works? If you remove the lines that you say create the issue, you still have this line: RewriteRule ^(.*)$ index.php?q=$1 [L,QSA] which is the one that handles rewriting urls to the form q=admin.
You could try moving the 2 lines of code:
RewriteCond %{HTTP_HOST} ^www.domain.com$
RewriteRule ^(.*)$ "http://domain.com/$1" [R=301,L]
To immediately below the 'RewriteEngine on' line (and obviously putting your domain in place of domain.com) so that they run first before the rest of the rules. This might work, but to me the above looks like it will be rewriting to q=admin anyway, so maybe this is a drupal setup issue that I am unfamiliar with.