Hi there,
We also have this problem, however we have Continuous Invoice Generation enabled under General Settings -> Invoices. This happens with all payment method types. I opened a ticket with WHMCS back in December of 2014 and they were unable to assist without me granting them access to our server.
It messes up our Income Forecast, otherwise it's not a huge deal since the client is billed properly.
Anyone else having this problem? Check by running the following query on your database:
SELECT * FROM `tblhosting` WHERE `nextduedate` <= CURDATE() AND `domainstatus` = 'active'
Jason