Thanks! I ended up toying around with stuff and figured out that checking “Skip Remuxing Files” brought things back in order.
As an aside, I wasn’t removing commercials or editing the video in any other way. The transcodes are straight conversions – MKV > MP4, x264 > x264, AC3 > AAC.
And, the subtitle shift varies from file to file, so it’s impossible to set a standard offset.