I was building a model for a client when I came across this issue, was going to a live demo and thankfully that got canceled. I've boiled it down to this simple model, but still have no clue what the issue is.
I have the model stop when the main conveyor empties for the various iterations.
Kept trying to get down to the root cause, but don't think I found it. Possibly something to do with conveyors coming off the main conveyor at an angle and it backing up to the transfer point.