Hi Steve,
unfortunately there is no option to disable start/stop messages in the Zaquencer.
Those messages are part of the Midi standard clock.
As you said, if there should be an option for it, it should be in the M32.
Some ideas regarding that topic can be found here:
http://forum.moogmusic.com/viewtopic.php?f=19&t=24452
Have you tried programming a blank sequence in the M32 sequencer so it doesn´t matter if it runs? One user writes:”I have created a empty sequence on M32 by entering a rest on step 1. Now when I start Live it does not go bongbongbong”
One user has a workaround: “disabling the m32 sequencer: Assignable OUT of M32 set to “step1 trigger” into Sequencer run/stop. The first note is played, then the seq. stops.”
You could also try to find a small midi filter box to filter out start/stop messages (make sure it can filter start/stop message types).
Hope I could give you some ideas.
Best,
Christian