If there are sequences that send notes on the “Master Channel”, CUIA may be triggered. There are some safeguards against this happening, e.g. we disable “Master Channel” by default and do not allow chains to be set to the “Master Channel” but this situation can sitll occur, e.g. if an older snapshot has such configuration or if you change the “Master Channel” to an already assigned MIDI channel.
It may be advantageous to avoid notes on the “Master Channel” reaching CUIA from the sequencer or SMF player. It may be worth raising a ticket about this in the issue tracker. I am sure this is likely to be the cause of the problem you had.