The warning means there is a gap or discontinuity in audio stream of the file. It usually happens on broken recording, but it could be a weirdly muxed file. In any case, unless I can get my hands on it I won't be able to tell what exactly is going on here.
It seems to effect all my other 10bit files too just not enough to be noticeable in playblack, usually it is -25ms on those instead of -41ms. Also if I push the audio by 41ms on the video on my ipad it fixes the sync for that episode.
Also it might be possible the ordered chapters are putting the audio sync off as the opening and ending cant be played in said file as they are ordered chapters, maybe supporting ordered chapters might fix it. Testing my 10bit files without ordered chapters are fine
Edit : It seems ordered chaptered files on their own are fine, the issue seems to be when ordered chapters + flac are in the same file interestingly enough 8bit files with ordered chapters + flac audio are off by 41ms and 10bit files with ordered chapters + flac audio are off by 25ms. Also it seems to always start to go out of sync about 10 seconds into each video represented in the log by
23:59:21 WARN 0D gst.audiotimestampcorrector AudioTimestampCorrector.c:217 Resyncing audio timestamps by -0.413299s, stream time: 0:00:10.496000000
I uploaded 2 files to your mediafire 1 called 8bit test file and 1 called 10bit test file they should show up there soon