Hi @mclass,
I have spent sometime this afternoon trying to recreate and resolve the issue you are experiencing, so far without success.
I setup topics in MQTT Explorer, like this:

- mclass_aeotec_mqtt_explorer.png (160.14 KiB) Viewed 2246 times
I setup all topics as retained with a QOS of 1.
I then setup a Hub based on qualia and then went to add a device and can do so successfully:

- mclass_aeotec_indigo_device.png (352.91 KiB) Viewed 2246 times
So, your definitions seem to work on my system.
I am beginning to clutch at straws, but here are some things I would check:
- make sure the qualia name in the Indigo Hub settings is in lowercase
- make sure that topics listed in MQTT Explorer show as retained (see image). You can normally test this by quitting MQTT Explorer and then launching MQTT Explorer again to check everything is still there and hasn't disappeared.
- In HE make sure that in the MQTT App > MQTT Publish Formats that Complete & compliant homie topics is on
I am obviously missing something in your mix but can't put my finger on it at the moment.
I am currently doing some major changes to the plugin but once these are relatively stable, I can PM you a link to the revised plugin for you to try. It will be a few days yet before I finish these changes.