Fees not applied to customer invoice

Hi there,
I’m wondering if I’ve missed an option in the settings area perhaps?

I’ve noticed that when I send an invoice to a customer and they use the ‘pay’ link in the email to be taken to my checkout there are no fees added regardless of the gateway the customer might choose.
Your plugin works perfectly on a normal purchase through the store though.

Any suggestions would be very much appreciated.

Kind regards,
JP