Issue
After updating the Default Form Template in Nintex Forms Management, duplicate controls appear on all default forms.
Resolution
This is expected behavior after changing the Default Form Template to a form with existing controls, as new forms will always pull in the list's columns as controls on the form.
Additional Information
The way that the template system works is that it pulls in default controls from the list in addition to the controls that already exist on the 'template' that is uploaded into SharePoint.
A blank Form Template which when uploaded will only pull in the default controls from the list (this means that no banner will be included and the controls will not be duplicated). Because attachments are on by default, the attachment control will be included in the form design, unless you disable attachments for the list.