In the edit item project window under the customer portal settings section, there are 3 custom field template options. They are; View, Add, and Edit field template settings. Please make sure that you are applying the desired custom templates on all three sections for the customer portal users.
The order of fields in a custom field template is different from the view in the windows client opposed to the customer portal view. If you are planning to use the same exact template view for the customer portal and for the windows client, then I would recommend of creating a duplicate template so that your field settings are different from each other.
Thank you,
Dragan Marceta
www.Axosoft.com