There appears to be an omission within the custom payment module docs.
It doesn't reference that you need to add an entry in to the CUSTOM_PAYMENT_MODULES list within local_settings.py
As per this note within the configuration system docs: http://www.satchmoproject.com/trac/wiki/ConfigurationSystem#Externalmodules
Just spent 20 minutes tearing my hair out!
Reported by MikeHowarth