When editing a membership Civi sends receipt and confirmation even with box unchecked
Have you checked that the mails are actually being sent out?

In civiCRM 4.6.4 I have found that I receive the following pop-up when editing a membership record with an attached contribution record (this does not seem to occur when there is no contribution recorded with the membership), but if the "Send Confirmation and Receipt" box is unchecked, no mails are actually sent out even though I got the message below.