You mean /themes/themename/mails/nl/?
  I have these .tpl (orderconfcartrules.tpl and orderconfproductlist.tpl ) files placed there.
  When the customer places an order, he receives an email with orderconf template - variables work properly 
Yes this works properly now. 
  When I manually send a message (using the same template) to the customer, the variables do not work 
Why should you manually send a message to the customer using this template ?