Hi there. I realized this is an old thread but I have also been struggling with the closed captions being in sync only after commercial cuts have been done. I have searched the internet for help and there are a couple of threads talking about it. This is one of them.
I’m not sure but I’m betting everyone is encoding into MP4 while doing the commercial cuts. That’s what i was doing and I tried adjusting the subtitles with the settings but it seems like, different shows and different movies behave differently. Sometimes being progressive, sometimes being just a couple seconds for the whole show, sometimes its like 20-30 seconds off.
I need my subtitles. I don’t read them all the time but sometimes I can’t understand what people are saying and want to see what they said.
The solution or workaround if you will, is to do the Comskip, and leave the Conversion profile to TS Unprocessed. Not sure why, but the Subtitles do not go out of sync this way. Then have your files placed into a temp folder. Where you can later convert them to mp4, as another task.
I use Plex and I just set it to watch my Temp Folder and my TV Shows folder so that way as soon as the commercials are cut I can watch the show and the show will still be there after it gets converted someday later.
Some additional info is that the Comskip and saving to temp folder only takes between 5-15 mins. My mp4 conversions with Comskip were taking 30-120 mins. So your shows are available with no commercials a lot quicker. If you want to watch them the same day you record them this is the way to go.