I have had this issue for a long time so it isn’t necessarily related to the latest release/kernel. I’m just finally getting around to trying to resolve it. I thought after reading this, Playback Video - sound stuttering after March 5th Update, that it sounded like my issue, but I’m already on the latest build so not sure if it’s related.
As the topic states, some movies play with frequent 5-15s stutter/pauses.
I have the PI3 hdmi’d to a samsung TV, ethernet to my Freenas (where all media is stored).
I don’t seem to have this issue with TV shows, though that could be just codec related, not sure.