The example posted for writing the configuration register was for what looks like an EZIO8SA. Can you run the same trace using your EZIO6I?
Many PC based products write links to PLMs. PowerHome2, HouseLinc2, the SHN Utility will but it cannot write link records to the same device it is using to communicate with the powerline. You would have to use the PLC as the powerline device for the SHN Utility for it to be able to write link records in the PLM. Also it seems like Indigo is dependent on the Broadcast message. If you have active links with the EZIO6I Inputs it will send Group messages rather than Broadcast messages.
They must be writing at least one link record in the PLM with the EZIO6I address as the PLM will not pass the Broadcast message back without it. The PLC might have but the PLM will not.
The only thing I can say is that my EZIO6I sends Broadcast messages for Input 1 and Input 5 when the Enable Analog Inputs and Broadcast Status Chg options are set in the Configuration Register. Have you double checked the wiring of the EZEye to be sure all 4 wires are connected to the correct EZIO6I pins. Not sure how bad wiring would cause the result but just trying to cover all bases.