I assume all the other apiarists pipes on that row are configured with combs going to blue rather than black? Or do you just have a pipe setup hidden by the ceiling in the last pic? If the latter, make sure you've got iron pipes set up to route bees in the appropriate direction.
Just from what we can see, though, your iron pipes are backwards. This causes the items to bounce backwards and when they reach the apiarist's pipe they find a junction where there are no legal exits (apiarist pipes will not bounce items back through the same way they entered) and will pop out at the apiarist pipe rather than at the iron pipe making it look like the apiarist pipe is the problem. Furthermore, they accelerate items quite a bit, so it's easy to miss the quick turnaround at the iron pipe.