Your issue is that you can't filter your shipping method regarding a zone using a custom field, but using the defaults address fields.
Sorry, I'm not understanding if you are telling me a solution, fact or stating my problem? If you are stating my problem then yes I am trying to filter a shipping method by using a custom field that is selecting shipping zones and it is not working.
Can you show us how you configured your custom zone through some screenshots ?
By Custom Zone do you mean the zone setting in System > Zones? The setup for this is shown in the image 02-zone.jpg.
If this is not correct then please specify the location of the screen shot you require (e.g. Display > custom fields > etc.)