From the symptoms you describe, this sounds related to the issue being tracked here: Samsung TV Plex App audio cuts out
Disabling Direct Play, and Direct Stream only disguises the root cause, and is generally agreed to be a short term fix for a larger problem. Disabling these options forces the server to transcode both the audio and video streams, resulting in a 100% compatible stream, therefore - no audio cutout. Transcoding will always result in some audio and video degradation, there is no way around it. But higher quality transcodes can be visually and aurally close enough to be imperceptibly different.
The reason some of your videos may have worked where others did not, is that they could have already been in the correct format, meaning that the audio was already 100% compatible to begin with.
There is no word on a fix as yet, but most people are doing the same thing as you, or have downgraded to a previous version of the Plex Server as a short term work around.
