In the remote chance someone else runs into this problem - if you've gotten a Poly Effects Hector or Beebo which shows the logo of the other device on startup:
- Go inside "QA Check" in the settings menu (where you set the MIDI channel)
- Click "Swap to Hector/Beebo", then "Back"
- Turn the module off and on again.
While they are firmware compatible, setting the Hector to the proper mode fixed missing outputs and CV generation for me.