I have some good news!
After re-reading over this thread, and a few others like It I was able to piece together enough common scenarios to reproduce this issue over a lengthy Saturday debugging session. It turns out there where more than one contributing factor (resuming/seeking, long periods where there was no subtitle dialog to be shown, and some start from the beginning timing issues) All manifested themselves in subtile ways that are not always reproducible, this is why I have struggled to reproduce when a number of you here suffer with the issue daily.
I understand many of you wished we had found and fixed this issue sooner, but this really has been hard to lock down in a reproducible manor to both validate the issue, and test the subsequent fixes as well.
Big thanks to this reply here Plex losing subtitle while playing - #422 by maclaustre (which helped narrow down how to reproduce) and @MR2DEVIL for your screenshot of John Wick which turns out was the perfect film to reproduce 
I have tested the fixes locally and I am working on getting a build for you guys to use in a few hours to confirm the fixes.
As previously mentioned, here are download links to an experimental build
The new Plex Media Server Beta 1.18.0.1846 contains all the subtitle fixes(and more) from the previous preview build shared in this forum.
Please feel free to upgrade.
