The links records are not correct or the Group numbers assigned to the Inputs are not correct. Something occurred when creating the second link record that overlaid the information used by the first set of link records or the link records themselves were overlaid.
Describe in detail what you did to create the links. Did Indigo create the links, did you use the Set button technique on both devices (cover the exact Set button sequence, how long held, how many times pressed to select the Input, etc), was indigo involved in creating either end of the links. If you run the SHN Utility it will show both the Group numbers assigned to the Inputs and the link records in the EZIO6I. It cannot display the link records in the PLM assuming you would be using the PLM as the powerline interface device for the SHN Utility.