Bumping a slightly old thread because this has also happened to me, but I have never been able to pinpoint it. I started recording my CB unkillable runs to see if I could find the variance, and fortunately I was able to see the change, though I cannot explain it. My unkillable success rate is about 95%, with only the occasional one popping up as a failure.
First of all, for those of you that are interested in recording your own game time, Windows 10 has a native inbuilt video recording feature in the xbox game bar, so you don't have to download any third party program. Just launch Raid, then press WindowsKey + Alt + R to start recording. A small little recording icon will come up after a few seconds and you can click stop whenever. The videos are saved into C:\Users\<username>\Videos\Captures. I learnt this while trying to capture videos of the issue.
Anyhoo, I have uploaded a video comparision into a really old youtube channel that I created back in 2009 to upload video checks for other games (which I have now since cleaned up). The raid video can be found at https://www.youtube.com/watch?v=rWlt3zOYcRU
The top part of the video is a successful run, while the bottom is a failed one. I have tried to keep the timings quite similar, but you will notice at the 1:29 mark there is a variance. Straight after CB uses Dark Nova and it starts turn 8, it goes HK, then OB, then the failed run goes Kael and Maneater, while the successful run goes Maneater and then Kael.
This minor sequence break changes the whole timing for the rest of the run, with the failed run finishing on turn 13. The speeds and gear of the champions remained unchanged, and infact the very next run after the failed one succeeded without issue. I can also confirm that none of the characters have any turn boosting masteries.