In flight I hit 0 for Main. I get a "Taxi to runway xx and hold short. Tower on nnnn. Delta xxxx." This doesn't happen all the time, however. But it does happen when Otto is flying and has the comms.

i'm sorry, i don't see anything with that clearance, off the top of my head. where is this happening?

That sounds like a missing ack that was repeating a ground clearance to the runway at departure time. Was it performed and read back by Otto as you started your taxi to the departure runway? Did you give comms to Otto between you receiving ground departure runway clearance but before it was acked?