I just solved this issue on my Roku Streaming Stick+ without rolling back the server version. From the Roku main menu (NOT within the Plex app) I went to Settings > Audio > HDMI > then disabled the “Auto Detect” function (I chose Dolby Digital/DTS instead).
Now when I watch Live TV or DVR, the Plex dashboard shows Direct Stream AC3 5.1 and my receiver indicates it’s receiving Dolby Digital. No more audio transcoding!
Just tried that on my Roku Ultra and still transcoding to MP3. Using Server 2012 as my OS and latest build of Plex.
tarfu7’s suggestion will only impact a few folks who’s equipment natively supports multichannel but Roku didn’t autodetect it (see more details about that from earlier posts).
If Roku can’t autodetect correctly, it will default to Stereo - if your equipment can support multichannel then setting it manually (or using passthrough) can help avoid the transcoding bug. Check your audio equipment support to verify which options might work for you.
Otherwise, you might benefit from downgrading the server as earlier posts suggest (or wait for a fix… hopefully soonish).
One note - if you do get AC3 support working (no transcoding) you might hit a Roku bug where AC3 audio can get delayed in which case turning off Direct Play is a workaround while we wait for Roku to fix that bug in their 9.4 OS.
We have released a Roku Preview version to transcode to AAC when necessary instead of MP3. This update will be in the next official update when approved.
@ljunkie - Thank you very much for the update! I went ahead and updated my Plex Preview channel and from the testing I did it looks like you guys are almost there! 7.1 AAC no longer transcodes to Stereo MP3 258kbps.
However, 7.1 AAC is now transcoding to Stereo AAC 258kbps instead. See below:
When I test a file that is using 5.1 AAC instead, it properly transcodes back to AC3 5.1 640kbps.
I believe 7.1 AAC should be transcoding to Surround AC3 640kbps instead of Stereo AAC 258kbps. I’m almost positive that’s how it was behaving before this all starting happening, 7.1 AAC > 5.1 AC3.
Again, very appreciative of your response and I hope my feedback is useful to hopefully make some tweaks for the final release. I did test as many files as I could on the preview channel and AC3, E-AC3, DTS all were direct playing just fine so it doesn’t seem to have broken any other kind of audio that I can tell. 
Edit: Just so I’m not being confusing anyone about bit-rates I confirmed bitrates in Plex Dash on my phone because the server dashboard nor Tautuli show them. 5.1 AAC to 640kbps AC3 works fine but 7.1 AAC is 258kbps and Stereo.
@flickyourbic I think I identified the issue, and I’m surprised it ever worked. From what I can tell it would have only worked (and does now) if your device supports EAC3 (DD+), otherwise it would be converted to 2ch audio. Previously it would have been converted to 2ch AAC instead of MP3, so maybe it was less noticeable up until recent. We’ve fixed the MP3/AAC bit, and I believe I have hold on the 7.1 AAC → 2ch AAC issue. I’ll update this thread when I have more info and hopefully a fix.
We have released another Preview update, v6.7.10, to fix the issue in the OP.
Looks like that did it! 7.1 AAC is now transcoding to 5.1 AC3 @ 640kbps. I can already tell the audio is much better now.
Thank you again for acknowledging and addressing this issue! I will be keeping an eye out for the official Plex Roku update and will use the preview channel in the meantime.
One thing that still kind of puzzles me though, my TCL TV running Roku didn’t have any issues during this entire time. It was only my Streaming Stick+ that was effected. The only difference is the TCL TV is using the onboard speakers and my Streaking Stick+ is using a receiver via optical audio.
You’re welcome! I’m glad we could figure this out. Note that this update didn’t make the cut for the next official release, so it will be in a release after that.
The bug only revealed itself when there wasn’t DD+ (EAC3) support, otherwise the audio would have been converted into EAC3. Missing DD+ is when it would be converted into 2ch audio.
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