>> On my Polysix, when I click the Arp button with the Arp trigger cable
>> connected, a sustained note always sounds. When the trigger is
>> deactivated by the uC, the note is there again. Is that normal?
For the CV that you send to the Arp Trigger jack, is it normally-low that pulses high for each note, or is it normally-high that pulses low for each note. If you're getting that sustain behavior, you might try coding it to be the other way.
(I'd check my Polysix, but it's buried behind another project at the moment. In a couple days I ought to be able to check.)
Nice work, and keep sharing!
Chip