No, it ONLY happens with Stalker Client NFPS, nowhere else. For example, I've run IPTV Simple Client with a different playlist and it was fine.
I'm running an S802 Amlogic, the 2GB RAM version. Kodi 15.2. However, the reason I don't think it's the box is that it only happens with certain channels. Non of the US channels do that, including the high traffic HBO, Showtime, etc, none of the American sports channels etc. So far in my testing, only the first 50 channels or so which are BBC, ITV, and then things like WWE Network (it's the worst on this particular channel, where it happens every 10-20 seconds).
It is DEFINITELY a strange buffering issue now that I've examined it closely, the buffering notification in the top right corner appears momentarily but the audio continues while the video jumps back a second or two, then double times forward to catch up to the audio.
edit: I'll try smaller groups as you mentioned as soon as I have a chance.