This was my experience too. Thanks for the suggestion. I tried a remux with just a track copy like you mentioned and it cleared up on one of my files.
Roku keeps messing up ac3 playback in MKV (9.4 had audio delay). 
I haven’t noticed any issues with MP4.
Hmm, I’ve not had an issue with AC3\MKV. I use handbreak 1.3.3 to encode my files with the original audio directly copied from the source (AC3 or DTS). Worth a try maybe?
So far I’ve not had any more issues with direct stream for the audio types posted above and the specific files that would consistently stutter have not been issue after remuxing. I’ve not seen any issues with dialogue out of sync either.
Plex Media Info from one of my AC3 files.
Codec H264
Bitrate 1541 kbps
Bit Depth 8
Chroma Location left
Chroma Subsampling 4:2:0
Coded Height 720
Coded Width 1280
Color Primaries bt709
Color Range tv
Color Space bt709
Color Trc bt709
Frame Rate 23.97599983215332 fps
Height 720
Level 4.0
Profile main
Ref Frames 4
Scan Type progressive
Width 1280
Display Title 720p (H.264)
Extended Display Title 720p (H.264)
Codec AC3
Channels 6
Bitrate 640 kbps
Language English
Audio Channel Layout 5.1(side)
Sampling Rate 48000 Hz
Title Surround
Display Title English (AC3 5.1)
Extended Display Title Surround (English AC3 5.1)
Below is what my setup looks like for reference, not that it should matter.
Roku: 4660X
SW: 10.0.0 B 4209-46
Plex Client:
6.8.3.7132-9d030676d-Plex
Plex Server:
Windows Server 2008R2
Plex Version 1.23.5.4801 Beta Channel
Dual Xeon L5639
Fast RAID array
Transcoder temporary directory on a ram disk.
Dual Gigabit
Bla Bla etc.
This was the part I was agreeing with… by redoing the mkv container (remuxing), one of my files was fixed as well. Since Roku had an acknowledged ac3/eac3 in mkv audio bug earlier this year it seems like a relevant data point. Maybe their fix isn’t complete or they introduced a new bug.
If anybody has before and after files, examples can be uploaded here that might help. That helped with that past audio bug. https://support.plex.tv/articles/201035968-generating-sample-files-from-media/
I already trashed my known broken ones but if I come across another I’ll upload here.
I see what you are saying now. I misinterpreted that it remuxing fixed one file but still had trouble with others after remuxing. 
Reading replies at 2:00am I guess isn’t my best ability. 
What’s the latest on this? Still having stuttering issues with Roku and Direct Playback. Will the OS 10.5 include any fixes for this? I’ve seen other threads talking about the same issue with Roku sticks.
Happens to me on an Ultra w/version 10.0.0 and AC-3. The video in question was 2 Mbps, too. I have a pretty decent box I’m running the server on, though it is in a docker container, not that it should matter.
"codec_long_name": "H.264 / AVC / MPEG-4 AVC / MPEG-4 part 10", "codec_long_name": "ATSC A/52B (AC-3, E-AC-3)",
Been happening for months on a lot of audio formats besides AAC with the built in workaround.
I recently discovered the same issue, specifically with AC3 2.0 (Stereo) tracks. I tried a few and they all stutter constantly every few seconds.
The only workaround is to disable Direct Play and allow the content to Direct Stream, and thankfully it seems to be working fine this way.
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