When trying to use HandBrakeCLI to take a clip from movie, I couldn't figure out why it was ignoring the durations in seconds I was defining with --start-at and --stop-at.
Turns out, you need to append the word "duration", "frame" or "pts" before each value. For example, to create a 20 second clip starting at the 1 minute mark:
HandBrakeCLI […] --startAt duration:60 --stop-at duration:20
Amazing what one can learn if one reads the manual page before wasting half an hour figuring out what's going wrong!