This happens to me and it's because at timed intervals of around 5-10 sec the bot sends/recieves a wave of information to the Pokemon go servers and this cause the lag spikes. For me I can play a game at 55ms then if Pokefarmer is running in the background at timed intervals it will send information in a big push which cause the lag spike. I reccomend that you just bot at night to prevent issues like this from happening to you. I can confirm this as I have Netbalancer installed and have monitored the network activity of Pokefarmer. For others this will be not be a problem as they will have high enough numbers for their download and upload speeds that it will act like a buffer and prevent the lag spike from happening but I since I have low download and upload speeds this affects me. Although you did say that it dosen't happen on your laptop maybe it was just a coincidence that it happens on your other device? You can google Netbalancer and download it for a free trial to temporary diagnose what may be causing you to lag on your other device.
