I'm near certain those issues are caused by your interface/codec/alsa config, not MOD 1.12 or pi-Stomp.
The MOD UI doesn't have fixed I/O (audio or MIDI). It presents the I/O that jack tells it about. If your interface has MIDI and alsa/jack know about it, it should likely show in MOD UI. You might try checking the alsa config file (/var/lib/alsa/asound.state) or the various alsa commands (amidi, aconnect, arecord, aplay, etc.)