Ah that explains it. It's weird though, that it doesn't do that with every video. Is it only arcadeitalia scrapes that are like that? Maybe I'll just scrape with UXS. Not sure how to use Handbrake.
How do I "manually scrape and specify the -convert_video option?"
EDIT:
I'm giving this a shoot before attempting something else:
https://retropie.org.uk/forum/topic/15764/script-retropie-convert-videos