No one has mentioned whether they are outputting the videos as .mp4 or .mkv ...
Cats4U
What do you think about me?
Of course, I've tested with updated ffmpeg, mp4box and mkvmerge
and mp4 (my default) as well as mkv (ffmpeg + mkvtoolnix) ..
.. never seen subs after finished
(also no change with update for linked nf subs remux into file error -
here)
@Pepe78Temple subs pt-PT =>
Sorry, but "Das Boot" s03 is currently not offered at SkyShowtime RO
In Browser Dev Tools - Network you can filter: webvtt
and can see/open/dl the subs (after selecting your subs language)

-= click pic to enlarge =-
or after downloading episode in SF you can search in StreamFab.log for: webvtt
and find the dl url for the subs - example Das Boot.s03e01 from your log -
here