I know the Polysix expects a Hi-Lo transition. I was using some weird trigger routines before with a couple of digitalWrites, so I'm not even sure I am using the Arduino correctly do to that.
Chris, it should work in Poly mode. Works for me. Unison is another story: your synth basically becomes mono, so every Arp trigger will trigger the attack and of course, since it's mono, will eat the release.
Enjoy,
Yash