Thanks for the info. I was confused with the scenario you described in the report but now can see that was the same scenario I was mentioning :)
Now, I've been trying to reproduce this bug in other machines and I have been unsuccessful. The only thing that I can think of right now which might be causing the issue according to  is:
"Note, however, that if the network device on the other side has auto-negotiation enabled (which is very common) and you turn auto-negotiation off, the other side will assume half-duplex mode and you will experience a significant loss of performance"
This means that if the router/switch you are connecting to has auto-negotiation enabled, and PowerNap disables it to change the speed, then the router/switch does something to adapt to the change in the machine, which might indeed cause the packet loss (router/switch cannot forward the packets till the NIC in the network device changes to half-duplex).
From previous studies, I recall that doing these changes might result in unreachable devices because of speed mismatch and the inability to establish a link (More info ). I personally believe that this might in fact be the issue (router/switch configuration). For now
sudo powernap-action --disable eth_speed
I will however, keep this bug open and try to reproduce this issue again. Thank again for the information. If you need anything else please feel free to contact me.