I bet it is a spoke nipple. Test your spokes by tapping each one gently with a screwdriver. They should all make a ringing sound. If one sounds different the nipple may have come off and is inside the rim.
You could try removing the dust caps from the jockey wheel, pulling the bearing seals, cleaning out the bearing, repacking with grease, and putting the seals back on. It is easy and worked for me.
I have noticed this as well. I don't know if it is associated with the firmware change or not. It is sort of irritating but I just ride and try to ignore it. Maybe the torque sensor is failing. Time will tell.
Happy Day!
Yes, update the software. The latest update is intended to protect the motor.
I changed the tires to Maxxis. I did not like the Butchers. Depends on where you ride though.
Enjoy.
I have the same bike. I replaced the 1199 cassette with the 1150. The 1150 has a steel 42t which I use a lot and is 1/3 the price. A bit heavier but I didn't care. It works fine.
The latest Park Tool chain cleaner 5.3 allows the handle to be put on either side. That means you can turn the cranks forward and clean the chain properly on an E-bike. Just keep your hands out of the spinning wheel.