As many users generate an invoice for their finance office or a third party for payment which is most often a wire or cheque payment, the handling fee is now added to invoices by default (What is your handling fee for wire and cheque payments and what is it for?).
However, the handling fee is not applicable if users pay by credit card and will automatically be deducted in case of a credit card payment. After credit card payment you will receive a receipt showing the invoice amount without handling fee.
To generate an invoice without handling fee, go to the invoice URL (http://www.jmir.org/payment/invoice/[ArticleID]) and click on the "credit card" payment option at the bottom.