When you add an email account to be checked by OnTime, there is a checkbox under 'New Item Settings' that reads 'Add Sender to Notification List'. I assume you checked this checkbox, which is why the customer gets notifications for items created through the email service.
There is currently no such setting for Customer Portal. What you'd have to do to notify the customer of changes in this case is either check the 'Notify the customer of changes made to this defect' checkbox on the add/edit defect page/window, which sends a one time notification, or add the customer to the notification list of the item or project.
I've added this as a feature request into our system for a future version.
Dan Suceava
http://www.axosoft.com