I have the same problem... how did you downgrade? I tried looking for a download and the version before 9.8 is listed as 9.6 on the HB website. Additionally the HB application date is the same on all my backups back to July but I only upgraded yesterday. Looks like some file was updated the application accesses rather than the application itself.
This may be a no-brainer, but make sure the DVD is clean. I had a couple Handbrake conversions fail recently (or just burn a few minutes of the movie). Ejecting the DVD and cleaning off the smudges with a soft cotton cloth (clean T-shirt might work) resulted in a good copy next time.
This is a DVD Iso on disc using DVDFab virtual drive so there's not actually a physical disc involved here. Like I said, this same file encoded absolutely fine day before yesterday. Very Strange.
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Hi for anyone else with this issue, I'm on Mac High Sierra, any videos that I was burning in SRT subtitles with Handbrake would ignore the first line of subtitle ONLY if the file was edited in Aegisub. I was able to reproduce issue this over and over. The SRT subtitle NOT edited by Aegisub did not give me this issue.
My only solution was to use Jubler which did not give me this issue. Good luck all.